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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathprint.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pathprint_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/pathprint.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 '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 whether package 'pathprint' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'pathprint' is deprecated and will be removed from Bioconductor
See 'C:/Users/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
* 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 ... 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 ...
** running examples for arch 'i386' ... 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: 0x35731698>
<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
** running examples for arch 'x64' ... 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: 0x0000000047fdb138>
<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: 2 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/pathprint.Rcheck/00check.log'
for details.