Multiple platform build/check report for BioC 3.11 - CHECK report for SVAPLSseq on tokay2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SVAPLSseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SVAPLSseq_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SVAPLSseq.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 'SVAPLSseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SVAPLSseq' version '1.14.0'
* 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 ... OK
* 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: 0x16bcb000>
<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: 0x0000000015b68fb0>
<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
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/SVAPLSseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SVAPLSseq_1.14.0.tar.gz && rm -rf SVAPLSseq.buildbin-libdir && mkdir SVAPLSseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SVAPLSseq.buildbin-libdir SVAPLSseq_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SVAPLSseq_1.14.0.zip && rm SVAPLSseq_1.14.0.tar.gz SVAPLSseq_1.14.0.zip
###
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100 59005  100 59005    0     0  1256k      0 --:--:-- --:--:-- --:--:-- 1477k

install for i386

* installing *source* package 'SVAPLSseq' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SVAPLSseq'
    finding HTML links ... done
    SVAPLSseq-package                       html  
    prop.vars                               html  
    pvs.adj                                 html  
    pvs.unadj                               html  
    sig.features                            html  
    sim.dat                                 html  
    surr                                    html  
    svplsSurr-class                         html  
    svplsSurr                               html  
    svplsTest-class                         html  
    svplsTest                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SVAPLSseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SVAPLSseq' as SVAPLSseq_1.14.0.zip
* DONE (SVAPLSseq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SVAPLSseq' successfully unpacked and MD5 sums checked

CHECK report for SVAPLSseq on tokay2

Summary

Command output

Installation output

Tests output

Example timings