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CHECK report for PGSEA on tokay1

This page was generated on 2021-05-06 12:32:44 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PGSEA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1333/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGSEA 1.64.0  (landing page)
Karl Dykema
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PGSEA
Branch: RELEASE_3_12
Last Commit: 0f5b621
Last Changed Date: 2020-10-27 10:30:45 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: PGSEA
Version: 1.64.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PGSEA_1.64.0.tar.gz
StartedAt: 2021-05-06 05:29:44 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:31:58 -0400 (Thu, 06 May 2021)
EllapsedTime: 133.4 seconds
RetCode: 1
Status:   ERROR   
CheckDir: PGSEA.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PGSEA_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PGSEA.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 '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 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 'C:/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
* 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
'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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x0f933ea8>
<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

** running examples for arch 'x64' ... 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: 0x000000001aed1870>
<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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/PGSEA.Rcheck/00check.log'
for details.


Installation output

PGSEA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/PGSEA_1.64.0.tar.gz && rm -rf PGSEA.buildbin-libdir && mkdir PGSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PGSEA.buildbin-libdir PGSEA_1.64.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL PGSEA_1.64.0.zip && rm PGSEA_1.64.0.tar.gz PGSEA_1.64.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  958k  100  958k    0     0  16.8M      0 --:--:-- --:--:-- --:--:-- 17.0M

install for i386

* installing *source* package 'PGSEA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
** help
*** installing help indices
  converting help for package 'PGSEA'
    finding HTML links ... done
    GOLUBmcs                                html  
    PGSEA                                   html  
    VAIgsc                                  html  
    VAImcs                                  html  
    aggregateExprs                          html  
    convertSmc                              html  
    editSmc                                 html  
    go2smc                                  html  
    kegg2smc                                html  
    nbEset                                  html  
    readGmt                                 html  
    readSmc                                 html  
    scanSmc                                 html  
    smcPlot                                 html  
    writeGmt                                html  
    writeSmc                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'PGSEA' ...
** testing if installed package can be loaded
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'PGSEA' as PGSEA_1.64.0.zip
* DONE (PGSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'PGSEA' successfully unpacked and MD5 sums checked

Tests output


Example timings

PGSEA.Rcheck/examples_i386/PGSEA-Ex.timings

nameusersystemelapsed
GOLUBmcs0.180.030.20
PGSEA0.450.040.50
VAIgsc0.870.090.97
VAImcs0.520.000.51

PGSEA.Rcheck/examples_x64/PGSEA-Ex.timings

nameusersystemelapsed
GOLUBmcs0.170.000.17
PGSEA0.520.030.55
VAIgsc0.860.100.95
VAImcs0.490.080.56