reb 1.66.0
Karl J. Dykema
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/reb |
| Branch: RELEASE_3_11 |
| Last Commit: 0c09abf |
| Last Changed Date: 2020-04-27 14:12:02 -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:reb.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings reb_1.66.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/reb.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 'reb/DESCRIPTION' ... OK
* this is package 'reb' version '1.66.0'
* 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 'reb' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
Missing object imported by a ':::' call: 'Biobase:::EXPRSET_DEPR_MSG'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MAP2chromLoc: warning in mget(subnames, env = chrEnv, ifnotfound =
NA): partial argument match of 'env' to 'envir'
rmAmbigMappings: warning in ls(env = get(package)): partial argument
match of 'env' to 'envir'
.genMeanMatrix: no visible global function definition for 't.test'
buildChromCytoband: no visible global function definition for 'new'
buildChromCytoband: no visible binding for global variable
'Hs.cytoband'
buildChromCytoband: no visible binding for global variable
'Rn.cytoband'
buildChromCytoband: no visible binding for global variable
'Mm.cytoband'
buildChromMap: no visible global function definition for 'new'
cgma: no visible binding for global variable 't.test'
cset2band: no visible global function definition for 'aggregate'
fromRevIsh: no visible binding for global variable 'vai.chr'
reb: no visible global function definition for 'supsmu'
reb: no visible global function definition for 'lowess'
reb: no visible global function definition for 'approx'
regmap: no visible global function definition for 'par'
regmap: no visible global function definition for 'layout'
regmap: no visible global function definition for 'image'
regmap: no visible global function definition for 'axis'
smoothByRegion: no visible global function definition for 'supsmu'
smoothByRegion: no visible global function definition for 'lowess'
smoothByRegion: no visible global function definition for 'approx'
summarizeByRegion: no visible binding for global variable 't.test'
tBinomTest: no visible global function definition for 'binom.test'
writeGFF3: no visible global function definition for 'write.table'
Undefined global functions or variables:
Hs.cytoband Mm.cytoband Rn.cytoband aggregate approx axis binom.test
image layout lowess new par supsmu t.test vai.chr write.table
Consider adding
importFrom("graphics", "axis", "image", "layout", "par")
importFrom("methods", "new")
importFrom("stats", "aggregate", "approx", "binom.test", "lowess",
"supsmu", "t.test")
importFrom("utils", "write.table")
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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/reb/libs/i386/reb.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/reb/libs/x64/reb.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'reb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cset2band
> ### Title: cset2band
> ### Aliases: cset2band
> ### Keywords: manip
>
> ### ** Examples
>
>
> data(mcr.eset)
> data(idiogramExample)
>
> ## Create a vector with the index of normal samples
> norms <- grep("MNC",colnames(mcr.eset@exprs))
>
> ## Smooth the data using the default 'movbin' method,
> ## with the normal samples as reference and median centering
> cset <- reb(mcr.eset@exprs,vai.chr,ref=norms,center=TRUE)
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
reb
--- call from context ---
reb(mcr.eset@exprs, vai.chr, ref = norms, center = TRUE)
--- call from argument ---
is.null(chrom) || is.na(chrom)
--- R stacktrace ---
where 1: reb(mcr.eset@exprs, vai.chr, ref = norms, center = TRUE)
--- value of length: 24 type: logical ---
[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
--- function from context ---
function (eset, genome, chrom = "ALL", ref = NULL, center = FALSE,
aggrfun = absMax, method = c("movbin", "supsmu", "lowess",
"movt"), ...)
{
if (chrom == "ALL") {
chrom <- names(attr(genome, "chromInfo"))
if (is.null(chrom) || is.na(chrom))
stop("chromLoc object does not contain any chromInfo\n")
}
else if (chrom == "arms") {
chrom <- genome@chromLocs$armList
}
else if (chrom == "bands") {
chrom <- genome@chromLocs$bandList
}
else if (chrom == "mb") {
chrom <- genome@chromLocs$mbList
}
if (class(eset) == "exprSet") {
exprs <- eset@exprs
.Deprecated(msg = Biobase:::EXPRSET_DEPR_MSG)
}
else if (class(eset) == "ExpressionSet")
exprs <- assayData(eset)$exprs
else exprs <- eset
if (!is.null(ref)) {
if (!is.numeric(ref))
stop("column index's required")
}
method <- match.arg(method)
if (!exists(method))
stop(sQuote(method), " is not found")
if (!is.null(ref)) {
cat("Creating ratios...", "\n")
ref_mean <- apply(exprs[, ref], 1, mean, na.rm = TRUE)
exprs <- sweep(exprs, 1, ref_mean, "-")
}
if (center)
exprs <- scale(exprs, scale = F)
temp.exprs <- matrix(ncol = ncol(exprs))
for (chr in chrom) {
uCG <- try(.usedChromExprs(exprs, genome, chr, aggrfun))
if (inherits(uCG, "try-error") || is.null(uCG))
next
if (ncol(uCG$exprs) != ncol(exprs))
next
locs <- uCG$locs
names(locs) <- uCG$simpleIDs
gx <- uCG$exprs
dix <- duplicated(locs)
if (sum(dix) & is.null(aggrfun) & method != "movbin") {
warning(sum(dix), " duplicate locations found...removing duplicates\n")
gx <- gx[!dix, ]
locs <- locs[!dix]
}
r.matrix <- matrix(NA, ncol = ncol(gx), nrow(gx))
colnames(r.matrix) <- colnames(gx)
rownames(r.matrix) <- names(locs)
for (i in c(1:ncol(gx))) {
nas <- is.finite(gx[, i])
x <- locs[nas]
y <- gx[nas, i]
sm <- try(switch(method, movbin = try(movbin(y, ...)),
supsmu = try(supsmu(x, y, ...)$y), lowess = try(lowess(x,
y, ...)$y), movt = try(movt(y, ...))), silent = FALSE)
if (!inherits(sm, "try-error")) {
aa <- try(approx(x, sm, xout = locs), silent = TRUE)
if (!inherits(aa, "try-error")) {
r.matrix[, i] <- aa$y
}
}
}
temp.exprs <- rbind(temp.exprs, r.matrix)
}
temp.exprs <- temp.exprs[-1, ]
return(temp.exprs)
}
<bytecode: 0x0c29c768>
<environment: namespace:reb>
--- function search by body ---
Function reb in namespace reb has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
** running examples for arch 'x64' ... ERROR
Running examples in 'reb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cset2band
> ### Title: cset2band
> ### Aliases: cset2band
> ### Keywords: manip
>
> ### ** Examples
>
>
> data(mcr.eset)
> data(idiogramExample)
>
> ## Create a vector with the index of normal samples
> norms <- grep("MNC",colnames(mcr.eset@exprs))
>
> ## Smooth the data using the default 'movbin' method,
> ## with the normal samples as reference and median centering
> cset <- reb(mcr.eset@exprs,vai.chr,ref=norms,center=TRUE)
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
reb
--- call from context ---
reb(mcr.eset@exprs, vai.chr, ref = norms, center = TRUE)
--- call from argument ---
is.null(chrom) || is.na(chrom)
--- R stacktrace ---
where 1: reb(mcr.eset@exprs, vai.chr, ref = norms, center = TRUE)
--- value of length: 24 type: logical ---
[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
--- function from context ---
function (eset, genome, chrom = "ALL", ref = NULL, center = FALSE,
aggrfun = absMax, method = c("movbin", "supsmu", "lowess",
"movt"), ...)
{
if (chrom == "ALL") {
chrom <- names(attr(genome, "chromInfo"))
if (is.null(chrom) || is.na(chrom))
stop("chromLoc object does not contain any chromInfo\n")
}
else if (chrom == "arms") {
chrom <- genome@chromLocs$armList
}
else if (chrom == "bands") {
chrom <- genome@chromLocs$bandList
}
else if (chrom == "mb") {
chrom <- genome@chromLocs$mbList
}
if (class(eset) == "exprSet") {
exprs <- eset@exprs
.Deprecated(msg = Biobase:::EXPRSET_DEPR_MSG)
}
else if (class(eset) == "ExpressionSet")
exprs <- assayData(eset)$exprs
else exprs <- eset
if (!is.null(ref)) {
if (!is.numeric(ref))
stop("column index's required")
}
method <- match.arg(method)
if (!exists(method))
stop(sQuote(method), " is not found")
if (!is.null(ref)) {
cat("Creating ratios...", "\n")
ref_mean <- apply(exprs[, ref], 1, mean, na.rm = TRUE)
exprs <- sweep(exprs, 1, ref_mean, "-")
}
if (center)
exprs <- scale(exprs, scale = F)
temp.exprs <- matrix(ncol = ncol(exprs))
for (chr in chrom) {
uCG <- try(.usedChromExprs(exprs, genome, chr, aggrfun))
if (inherits(uCG, "try-error") || is.null(uCG))
next
if (ncol(uCG$exprs) != ncol(exprs))
next
locs <- uCG$locs
names(locs) <- uCG$simpleIDs
gx <- uCG$exprs
dix <- duplicated(locs)
if (sum(dix) & is.null(aggrfun) & method != "movbin") {
warning(sum(dix), " duplicate locations found...removing duplicates\n")
gx <- gx[!dix, ]
locs <- locs[!dix]
}
r.matrix <- matrix(NA, ncol = ncol(gx), nrow(gx))
colnames(r.matrix) <- colnames(gx)
rownames(r.matrix) <- names(locs)
for (i in c(1:ncol(gx))) {
nas <- is.finite(gx[, i])
x <- locs[nas]
y <- gx[nas, i]
sm <- try(switch(method, movbin = try(movbin(y, ...)),
supsmu = try(supsmu(x, y, ...)$y), lowess = try(lowess(x,
y, ...)$y), movt = try(movt(y, ...))), silent = FALSE)
if (!inherits(sm, "try-error")) {
aa <- try(approx(x, sm, xout = locs), silent = TRUE)
if (!inherits(aa, "try-error")) {
r.matrix[, i] <- aa$y
}
}
}
temp.exprs <- rbind(temp.exprs, r.matrix)
}
temp.exprs <- temp.exprs[-1, ]
return(temp.exprs)
}
<bytecode: 0x000000001724df30>
<environment: namespace:reb>
--- function search by body ---
Function reb in namespace reb 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/reb.Rcheck/00check.log'
for details.