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This page was generated on 2021-12-06 13:04:54 -0500 (Mon, 06 Dec 2021).

BUILD results for CelliD on nebbiolo2

To the developers/maintainers of the CelliD package:
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raw results

Package 267/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CelliD 1.2.0  (landing page)
Akira Cortal
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/CelliD
git_branch: RELEASE_3_14
git_last_commit: f2d8e5c
git_last_commit_date: 2021-10-26 13:07:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: CelliD
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CelliD
StartedAt: 2021-12-05 04:05:46 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 04:15:41 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 594.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CelliD
###
##############################################################################
##############################################################################


* checking for file ‘CelliD/DESCRIPTION’ ... OK
* preparing ‘CelliD’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘BioconductorVignette.Rmd’ using rmarkdown
Loading required package: Seurat
Attaching SeuratObject
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
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, 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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:SeuratObject':

    Assays

The following object is masked from 'package:Seurat':

    Assays

Registered S3 method overwritten by 'cli':
  method     from         
  print.boxx spatstat.geom
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.6     ✔ dplyr   1.0.7
✔ tidyr   1.1.4     ✔ stringr 1.4.0
✔ readr   2.1.1     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position()
✖ dplyr::collapse()   masks IRanges::collapse()
✖ dplyr::combine()    masks Biobase::combine(), BiocGenerics::combine()
✖ dplyr::count()      masks matrixStats::count()
✖ dplyr::desc()       masks IRanges::desc()
✖ tidyr::expand()     masks S4Vectors::expand()
✖ dplyr::filter()     masks stats::filter()
✖ dplyr::first()      masks S4Vectors::first()
✖ dplyr::lag()        masks stats::lag()
✖ purrr::reduce()     masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()     masks S4Vectors::rename()
✖ dplyr::slice()      masks IRanges::slice()
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Computing Fuzzy Matrix
Computing SVD
Computing Coordinates
PC_ 1 
Positive:  CHGA, ABCC8, SLC7A8, PEMT, MAFB, CRYBA2, HEPACAM2, GAD2, RFX6, SCGB2A1 
	   SSTR2, G6PC2, KCNK16, SLC38A4, RGS4, SEZ6L, VGF, PCP4, KCNMA1, KCTD12 
	   RGS9, FEV, EDIL3, SERPINI1, SMOC1, MLLT11, SPTSSB, HOPX, ADAMTSL2, LOXL4 
Negative:  IFITM3, LGALS3, TACSTD2, SERPING1, KRT7, RHOC, PRSS8, CDC42EP1, S100A11, LCN2 
	   CTSH, PPIC, ANXA4, SDC4, CLDN1, SERPINA3, SAT1, LAD1, ZFP36L1, TMSB4X 
	   LITAF, KRT19, ABCC3, KRT18, CFB, CAV2, TM4SF1, SERPINA5, TPM1, SLC44A2 
PC_ 2 
Positive:  KRT8, CD24, ELF3, CLDN4, LCN2, KRT18, GATM, CFB, SERPINA3, RAB11FIP1 
	   PRSS8, SLC44A4, GPX2, SDC4, TACSTD2, GJB1, ABCC3, CLDN3, PIGR, AMBP 
	   SERPINA5, MUC1, ANXA4, KRT7, CLDN10, KIAA1522, ERBB3, LAD1, CYP3A5, CLMN 
Negative:  SPARC, COL1A2, BGN, COL3A1, PDGFRB, COL6A3, COL1A1, COL15A1, COL5A1, NID1 
	   SFRP2, COL6A2, COL4A1, CDH11, LUM, MMP2, COL5A2, DCN, CYGB, TIMP3 
	   THBS2, F2R, LRRC32, IGFBP4, AEBP1, MXRA8, PXDN, SRPX2, MFGE8, THY1 
PC_ 3 
Positive:  IGFBP7, CFTR, AQP1, VTCN1, DCDC2, SPP1, TINAGL1, MMP7, TIMP1, ALDH1A3 
	   CMTM7, SERPINA1, PFKP, PMEPA1, KRT23, KRT19, HSD17B2, TSPAN8, S100A14, SLC3A1 
	   FUT3, NRP1, TFPI2, SLC34A2, ONECUT2, PROM1, CEACAM7, SLC4A4, PDGFD, CCND1 
Negative:  CTRB1, CPA2, CTRB2, CTRC, REG1B, PNLIP, PRSS1, PLA2G1B, PRSS3, CPA1 
	   CELA2A, PNLIPRP1, BCAT1, CELA3A, KLK1, DPEP1, REG3A, RARRES2, PDIA2, CPB1 
	   CELA3B, FAM129A, SLC39A5, ALB, GSTA2, CEL, REG3G, SPINK1, MT1G, REG1A 
PC_ 4 
Positive:  COL3A1, COL6A3, PCOLCE, COL1A2, COL5A1, LUM, DCN, THBS2, SFRP2, COL1A1 
	   MXRA8, PDGFRB, CDH11, COL5A2, GGT5, VCAN, LTBP2, ISLR, FMOD, VSTM4 
	   TPM2, LAMC3, COL6A1, EDNRA, IGFBP5, BGN, SPON1, ITGA11, CYGB, CRISPLD2 
Negative:  PLVAP, PECAM1, RGCC, FLT1, S1PR1, PODXL, KDR, ESAM, ERG, CXCR4 
	   MYCT1, CLEC14A, ECSCR, ESM1, PASK, CDH5, CALCRL, ROBO4, VWF, CD93 
	   PRDM1, GMFG, ACVRL1, GPR4, ANGPT2, TIE1, F2RL3, MMRN2, ABI3, TM4SF18 
PC_ 5 
Positive:  HADH, INS, IAPP, PDX1, PCSK1, NPTX2, CASR, SCD5, C1orf127, ADCYAP1 
	   WSCD2, PFKFB2, RBP4, SAMD11, BMP5, DLK1, ENTPD3, PRSS23, GPM6A, CYYR1 
	   GSN, RGS16, IGSF1, CADM1, CAPN13, VAT1L, GAD2, FFAR4, ASB9, TMEM37 
Negative:  LOXL4, FXYD5, FAP, CRYBA2, SMIM24, VGF, DPP4, SERPINE2, HLA-E, RGS4 
	   KCTD12, SLC38A4, PAPPA2, PLCE1, COTL1, FEV, HMGB3, SMOC1, SPOCK3, IGFBP2 
	   ARRDC4, CRH, PYROXD2, MUC13, NPNT, PPP2R2B, FAM84A, SYNDIG1, EGFL7, APOH 
04:14:57 UMAP embedding parameters a = 0.9922 b = 1.112
04:14:57 Read 2168 rows and found 30 numeric columns
04:14:57 Using Annoy for neighbor search, n_neighbors = 30
04:14:57 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
04:14:58 Writing NN index file to temp file /tmp/RtmpexgqGH/file22a33a10b1d6c0
04:14:58 Searching Annoy index using 1 thread, search_k = 3000
04:14:58 Annoy recall = 100%
04:14:59 Commencing smooth kNN distance calibration using 1 thread
04:15:01 Initializing from normalized Laplacian + noise
04:15:01 Commencing optimization for 500 epochs, with 84602 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
04:15:04 Optimization finished
Quitting from lines 301-329 (BioconductorVignette.Rmd) 
Error: processing vignette 'BioconductorVignette.Rmd' failed with diagnostics:
values must be length 1,
 but FUN(X[[2]]) result is length 0
--- failed re-building ‘BioconductorVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘BioconductorVignette.Rmd’

Error: Vignette re-building failed.
Execution halted