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CHECK report for pathprint on malbec1

This page was generated on 2021-05-05 12:10:28 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the pathprint package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1306/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathprint 1.20.0  (landing page)
Sokratis Kariotis
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/pathprint
Branch: RELEASE_3_12
Last Commit: c7e4ddd
Last Changed Date: 2020-10-27 11:22:19 -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: pathprint
Version: 1.20.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pathprint_1.20.0.tar.gz
StartedAt: 2021-05-05 04:22:40 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 04:24:23 -0400 (Wed, 05 May 2021)
EllapsedTime: 103.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: pathprint.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pathprint_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/pathprint.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathprint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathprint’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘pathprint’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'pathprint' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/pathprint.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
* 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 ... NOTE
exprs2fingerprint: no visible binding for global variable ‘chipframe’
exprs2fingerprint: no visible binding for global variable ‘genesets’
thresholdFingerprint: no visible binding for global variable
  ‘platform.thresholds’
Undefined global functions or variables:
  chipframe genesets platform.thresholds
* 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 ... ERROR
Running examples in ‘pathprint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diffPathways
> ### Title: Detect differentially activated pathways between fingerprints
> ### Aliases: diffPathways
> 
> ### ** Examples
> 
> require(pathprintGEOData)
Loading required package: pathprintGEOData
Warning: Package 'pathprintGEOData' is deprecated and will be removed from
  Bioconductor version 3.13
> 
> # Use ALL dataset as an example
> 
> require(ALL)
Loading required package: ALL
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> data(ALL)
> annotation(ALL)
[1] "hgu95av2"
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from ‘package:Biobase’:

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> # load  the data
> data(SummarizedExperimentGEO)
> 
> ds = c("chipframe", "genesets","pathprint.Hs.gs",
+     "platform.thresholds","pluripotents.frame")
> data(list = ds)
> 
> # extract part of the GEO.fingerprint.matrix and GEO.metadata.matrix
> GEO.fingerprint.matrix = assays(geo_sum_data[,300000:350000])$fingerprint
> GEO.metadata.matrix = colData(geo_sum_data[,300000:350000])
> 
> # free up space by removing the geo_sum_data object
> remove(geo_sum_data)
> 
> # The chip used was the Affymetrix Human Genome U95 Version 2 Array
> # The correspending GEO ID is GPL8300
> 
> # Analyze patients with ALL1/AF4 and BCR/ABL translocations
> ALL.eset <- ALL[, ALL$mol.biol %in% c("BCR/ABL", "ALL1/AF4")]
> ALL.exprs<-exprs(ALL.eset)
> 
> patient.type<-as.character(ALL$mol.biol[
+     ALL$mol.biol %in% c("BCR/ABL", "ALL1/AF4")])
> 
> # Process fingerprints
> ALL.fingerprint<-exprs2fingerprint(exprs = ALL.exprs,
+     platform = "GPL8300",
+     species = "human",
+     progressBar = TRUE
+ )
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
pathprint
 --- call from context --- 
exprs2fingerprint(exprs = ALL.exprs, platform = "GPL8300", species = "human", 
    progressBar = TRUE)
 --- call from argument --- 
if (class(exprs) == "ExpressionSet") {
    exprs = exprs(exprs)
}
 --- R stacktrace ---
where 1: exprs2fingerprint(exprs = ALL.exprs, platform = "GPL8300", species = "human", 
    progressBar = TRUE)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (exprs, platform, species, progressBar = TRUE) 
{
    if (class(exprs) == "ExpressionSet") {
        exprs = exprs(exprs)
    }
    if (!(platform %in% names(chipframe))) 
        stop("Platform name is invalid or not currently supported")
    if (!(species %in% names(genesets))) 
        stop("Species name invalid or not supported")
    gsdb <- get(genesets[species])
    print("Running fingerprint")
    geo.ann <- customCDFAnn(exprs, chipframe[[platform]]$ann)
    SCE <- single.chip.enrichment(exprs = geo.ann, geneset = gsdb, 
        transformation = "squared.rank", statistic = "mean", 
        normalizedScore = FALSE, progressBar = progressBar)
    SCE.threshold <- thresholdFingerprint(SCE = SCE, platform = platform)
    return(SCE.threshold)
}
<bytecode: 0x55cd43da6f50>
<environment: namespace:pathprint>
 --- function search by body ---
Function exprs2fingerprint in namespace pathprint 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: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/pathprint.Rcheck/00check.log’
for details.


Installation output

pathprint.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL pathprint
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘pathprint’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'pathprint' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'pathprint' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (pathprint)

Tests output


Example timings

pathprint.Rcheck/pathprint-Ex.timings

nameusersystemelapsed
consensusDistance24.508 1.35226.330
consensusFingerprint16.768 0.82417.626
customCDFAnn18.184 0.54418.784