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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PGSEA_1.64.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/PGSEA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PGSEA’ version ‘1.64.0’
* 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 ‘PGSEA’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/PGSEA.Rcheck/00install.out’ for details.
* 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
* 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
'library' or 'require' calls to packages already attached by Depends:
‘GO.db’ ‘KEGG.db’
Please remove these calls from your code.
'library' or 'require' call to ‘org.Hs.eg.db’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘GO.db’ ‘KEGG.db’ ‘annaffy’ ‘methods’
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
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
partial argument match of 'env' to 'envir'
PGSEA: no visible global function definition for ‘is’
PGSEA: no visible binding for global variable ‘t.test’
PGSEA: no visible binding for global variable ‘sd’
PGSEA: no visible global function definition for ‘pnorm’
aggregateExprs: no visible global function definition for ‘is’
aggregateExprs: no visible global function definition for ‘aggregate’
convertSmc: no visible global function definition for ‘read.delim’
go2smc: no visible binding for global variable ‘GOTERM’
go2smc: no visible binding for global variable ‘org.Hs.egGO2ALLEGS’
go2smc: no visible global function definition for ‘new’
kegg2smc: no visible binding for global variable ‘KEGGPATHNAME2ID’
kegg2smc: no visible binding for global variable ‘KEGGPATHID2EXTID’
kegg2smc: no visible global function definition for ‘new’
readGmt: no visible global function definition for ‘new’
readSmc: no visible global function definition for ‘new’
smcPlot: no visible global function definition for ‘par’
smcPlot: no visible global function definition for ‘hclust’
smcPlot: no visible global function definition for ‘dist’
smcPlot: no visible global function definition for ‘image’
smcPlot: no visible global function definition for ‘grid’
smcPlot: no visible global function definition for ‘axis’
smcPlot: no visible global function definition for ‘abline’
smcPlot: no visible global function definition for ‘box’
writeSmc: no visible global function definition for ‘write.table’
Undefined global functions or variables:
GOTERM KEGGPATHID2EXTID KEGGPATHNAME2ID abline aggregate axis box
dist grid hclust image is new org.Hs.egGO2ALLEGS par pnorm read.delim
sd t.test write.table
Consider adding
importFrom("graphics", "abline", "axis", "box", "grid", "image", "par")
importFrom("methods", "is", "new")
importFrom("stats", "aggregate", "dist", "hclust", "pnorm", "sd",
"t.test")
importFrom("utils", "read.delim", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PGSEA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aggregateExprs
> ### Title: Aggregate expression data
> ### Aliases: aggregateExprs
> ### Keywords: datasets
>
> ### ** Examples
>
> if (require(hgu95av2.db) & require(annaffy)) {
+ library(annaffy)
+ data(aafExpr)
+ class(exprs(aafExpr))
+ exprs(aafExpr)[1:4, 1:4]
+
+ #list possible values for the "using" argument
+ ls(pos=which(search()=="package:hgu95av2.db"))
+
+ convert <- aggregateExprs(exprs(aafExpr),"hgu95av2.db",FUN=mean,na.rm=TRUE)
+ convert[1:4,1:4]
+ }
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
PGSEA
--- call from context ---
aggregateExprs(exprs(aafExpr), "hgu95av2.db", FUN = mean, na.rm = TRUE)
--- call from argument ---
class(x) != "matrix" && !is(x, "ExpressionSet")
--- R stacktrace ---
where 1: aggregateExprs(exprs(aafExpr), "hgu95av2.db", FUN = mean, na.rm = TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (x, package = "hgu133plus2", using = "ENTREZID", FUN,
...)
{
if (class(x) != "matrix" && !is(x, "ExpressionSet"))
stop("need matrix or ExpressionSet")
if (is.null(package) && is(x, "ExpressionSet"))
package <- annotation(x)
if (is.null(package))
stop("annotation package name is required")
if (!require(package, character.only = TRUE))
stop(package, " is not available")
pPos <- paste("package", package, sep = ":")
if (length(grep(".*db", package)))
package <- gsub(".db", "", package)
nEnv <- paste(package, using, sep = "")
Env <- get(nEnv, pos = pPos)
if (is(x, "ExpressionSet")) {
ids <- featureNames(x)
x <- exprs(x)
}
else {
ids <- rownames(x)
}
lls <- mget(ids, env = Env, ifnotfound = NA)
if (length(lls) != length(unlist(lls)))
for (i in 1:length(lls)) lls[[i]] <- lls[[i]][1]
lls <- unlist(lls)
f <- factor(lls)
undupx <- aggregate(x, by = list(f), FUN, ...)
rownames(undupx) <- as.character(undupx[, 1])
undupx <- as.matrix(undupx[, -1])
return(undupx)
}
<bytecode: 0x7fb608bdcac0>
<environment: namespace:PGSEA>
--- function search by body ---
Function aggregateExprs in namespace PGSEA 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/PGSEA.Rcheck/00check.log’
for details.