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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SPIA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SPIA_2.51.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SPIA.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SPIA/DESCRIPTION’ ... OK
* this is package ‘SPIA’ version ‘2.51.0’
* 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 ‘SPIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: ‘KEGGgraph’
  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
combfunc: no visible global function definition for ‘na.omit’
combfunc: no visible global function definition for ‘pnorm’
combfunc: no visible global function definition for ‘qnorm’
getP2: no visible global function definition for ‘qchisq’
getP2: no visible global function definition for ‘pnorm’
getP2: no visible global function definition for ‘qnorm’
makeSPIAdata: no visible global function definition for ‘parseKGML’
makeSPIAdata: no visible global function definition for ‘nodes’
makeSPIAdata: no visible global function definition for ‘na.omit’
makeSPIAdata: no visible global function definition for ‘edges’
plotP: no visible global function definition for ‘na.omit’
plotP: no visible global function definition for ‘pnorm’
plotP: no visible global function definition for ‘qnorm’
plotP: no visible global function definition for ‘text’
spia: no visible global function definition for ‘pdf’
spia: no visible global function definition for ‘par’
spia: no visible global function definition for ‘phyper’
spia: no visible global function definition for ‘median’
spia: no visible global function definition for ‘sd’
spia: no visible global function definition for ‘density’
spia: no visible global function definition for ‘dev.off’
spia: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  density dev.off edges median na.omit nodes p.adjust par parseKGML pdf
  phyper pnorm qchisq qnorm sd text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "text")
  importFrom("stats", "density", "median", "na.omit", "p.adjust",
             "phyper", "pnorm", "qchisq", "qnorm", "sd")
to your NAMESPACE file.
* 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 ‘SPIA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spia
> ### Title: Signaling Pathway Impact Analysis (SPIA) based on
> ###   over-representation and signaling perturbations accumulation
> ### Aliases: spia
> ### Keywords: nonparametric methods
> 
> ### ** Examples
> 
> # Example using a colorectal cancer dataset obtained using Affymetrix geneChip technology (GEE GSE4107).
> # Suppose that proper preprocessing was performed and a two group moderated t-test was applied. The topTable 
> # result from limma package for this data set is called "top".
> #The following lines will annotate each probeset to an entrez ID identifier, will keep the most significant probeset for each 
> #gene ID and retain those with FDR<0.05 as differentially expressed.
> #You can run these lines if hgu133plus2.db package is available
> 
> #data(colorectalcancer)
> #x <- hgu133plus2ENTREZID 
> #top$ENTREZ<-unlist(as.list(x[top$ID]))
> #top<-top[!is.na(top$ENTREZ),]
> #top<-top[!duplicated(top$ENTREZ),]
> #tg1<-top[top$adj.P.Val<0.1,]
> #DE_Colorectal=tg1$logFC
> #names(DE_Colorectal)<-as.vector(tg1$ENTREZ)
> #ALL_Colorectal=top$ENTREZ
> 
> data(colorectalcancer)
> 
> # pathway analysis using SPIA; # use nB=2000 or higher for more accurate results
> #uses older version of KEGG signalimng pathways graphs
> res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",beta=NULL,nB=2000,plots=FALSE, verbose=TRUE,combine="fisher")

Done pathway 1 : RNA transport..
Done pathway 2 : RNA degradation..
Done pathway 3 : PPAR signaling pathway..
Done pathway 4 : Fanconi anemia pathway..
Done pathway 5 : MAPK signaling pathway..
Done pathway 6 : ErbB signaling pathway..
Done pathway 7 : Calcium signaling pathway..
Done pathway 8 : Cytokine-cytokine receptor int..
Done pathway 9 : Chemokine signaling pathway..
Done pathway 10 : NF-kappa B signaling pathway..
Done pathway 11 : Phosphatidylinositol signaling..
Done pathway 12 : Neuroactive ligand-receptor in..
Done pathway 13 : Cell cycle..
Done pathway 14 : Oocyte meiosis..
Done pathway 15 : p53 signaling pathway..
Done pathway 16 : Sulfur relay system..
Done pathway 17 : SNARE interactions in vesicula..
Done pathway 18 : Regulation of autophagy..
Done pathway 19 : Protein processing in endoplas..
Done pathway 20 : Lysosome..
Done pathway 21 : mTOR signaling pathway..
Done pathway 22 : Apoptosis..
Done pathway 23 : Vascular smooth muscle contrac..
Done pathway 24 : Wnt signaling pathway..
Done pathway 25 : Dorso-ventral axis formation..
Done pathway 26 : Notch signaling pathway..
Done pathway 27 : Hedgehog signaling pathway..
Done pathway 28 : TGF-beta signaling pathway..
Done pathway 29 : Axon guidance..
Done pathway 30 : VEGF signaling pathway..
Done pathway 31 : Osteoclast differentiation..
Done pathway 32 : Focal adhesion..
Done pathway 33 : ECM-receptor interaction..
Done pathway 34 : Cell adhesion molecules (CAMs)..
Done pathway 35 : Adherens junction..
Done pathway 36 : Tight junction..
Done pathway 37 : Gap junction..
Done pathway 38 : Complement and coagulation cas..
Done pathway 39 : Antigen processing and present..
Done pathway 40 : Toll-like receptor signaling p..
Done pathway 41 : NOD-like receptor signaling pa..
Done pathway 42 : RIG-I-like receptor signaling ..
Done pathway 43 : Cytosolic DNA-sensing pathway..
Done pathway 44 : Jak-STAT signaling pathway..
Done pathway 45 : Natural killer cell mediated c..
Done pathway 46 : T cell receptor signaling path..
Done pathway 47 : B cell receptor signaling path..
Done pathway 48 : Fc epsilon RI signaling pathwa..
Done pathway 49 : Fc gamma R-mediated phagocytos..
Done pathway 50 : Leukocyte transendothelial mig..
Done pathway 51 : Intestinal immune network for ..
Done pathway 52 : Circadian rhythm - mammal..
Done pathway 53 : Long-term potentiation..
Done pathway 54 : Neurotrophin signaling pathway..
Done pathway 55 : Retrograde endocannabinoid sig..
Done pathway 56 : Glutamatergic synapse..
Done pathway 57 : Cholinergic synapse..
Done pathway 58 : Serotonergic synapse..
Done pathway 59 : GABAergic synapse..
Done pathway 60 : Dopaminergic synapse..
Done pathway 61 : Long-term depression..
Done pathway 62 : Olfactory transduction..
Done pathway 63 : Taste transduction..
Done pathway 64 : Phototransduction..
Done pathway 65 : Regulation of actin cytoskelet..
Done pathway 66 : Insulin signaling pathway..
Done pathway 67 : GnRH signaling pathway..
Done pathway 68 : Progesterone-mediated oocyte m..
Done pathway 69 : Melanogenesis..
Done pathway 70 : Adipocytokine signaling pathwa..
Done pathway 71 : Type II diabetes mellitus..
Done pathway 72 : Type I diabetes mellitus..
Done pathway 73 : Maturity onset diabetes of the..
Done pathway 74 : Aldosterone-regulated sodium r..
Done pathway 75 : Endocrine and other factor-reg..
Done pathway 76 : Vasopressin-regulated water re..
Done pathway 77 : Salivary secretion..
Done pathway 78 : Gastric acid secretion..
Done pathway 79 : Pancreatic secretion..
Done pathway 80 : Carbohydrate digestion and abs..
Done pathway 81 : Bile secretion..
Done pathway 82 : Mineral absorption..
Done pathway 83 : Alzheimer's disease..
Done pathway 84 : Parkinson's disease..
Done pathway 85 : Amyotrophic lateral sclerosis ..
Done pathway 86 : Huntington's disease..
Done pathway 87 : Prion diseases..
Done pathway 88 : Cocaine addiction..
Done pathway 89 : Amphetamine addiction..
Done pathway 90 : Morphine addiction..
Done pathway 91 : Alcoholism..
Done pathway 92 : Bacterial invasion of epitheli..
Done pathway 93 : Vibrio cholerae infection..
Done pathway 94 : Epithelial cell signaling in H..
Done pathway 95 : Pathogenic Escherichia coli in..
Done pathway 96 : Shigellosis..
Done pathway 97 : Salmonella infection..
Done pathway 98 : Pertussis..
Done pathway 99 : Legionellosis..
Done pathway 100 : Leishmaniasis..
Done pathway 101 : Chagas disease (American trypa..
Done pathway 102 : African trypanosomiasis..
Done pathway 103 : Malaria..
Done pathway 104 : Toxoplasmosis..
Done pathway 105 : Amoebiasis..
Done pathway 106 : Staphylococcus aureus infectio..
Done pathway 107 : Tuberculosis..
Done pathway 108 : Hepatitis C..
Done pathway 109 : Measles..
Done pathway 110 : Influenza A..Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SPIA.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘SPIA.Rnw’
  ...
> ALL_Colorectal[1:10]
 [1] "3491"  "2353"  "1958"  "1843"  "3725"  "23645" "9510"  "84869" "7432" 
[10] "1490" 

> res = spia(de = DE_Colorectal, all = ALL_Colorectal, 
+     organism = "hsa", nB = 2000, plots = FALSE, beta = NULL, 
+     combine = "fisher", verb .... [TRUNCATED] 
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘SPIA.Rnw’ using Sweave
Loading required package: KEGGgraph

Attaching package: ‘KEGGgraph’

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

    plot

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

    plot

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, 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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: org.Hs.eg.db


Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SPIA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SPIA
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SPIA’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SPIA)