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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Spaniel
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* checking for file ‘Spaniel/DESCRIPTION’ ... OK
* preparing ‘Spaniel’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘spaniel-vignette.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
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
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
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
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:matrixStats':
count
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Warning in spanielPlot(object = seuratObj, grob = image, plotType = "NoGenes", :
NAs introduced by coercion
Warning: Removed 6 rows containing missing values (geom_point).
Warning in spanielPlot(object = seuratFiltered, grob = image, plotType = "NoGenes") :
NAs introduced by coercion
Warning in spanielPlot(object = seuratFiltered, grob = image, plotType = "NoGenes") :
NAs introduced by coercion
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
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|======================================================================| 100%
PC_ 1
Positive: mt-Rnr1, mt-Nd5, mt-Co1, mt-Nd2, Selenop, S100a5, Omp, Ptn, Nr2f2, Sash1
Igfbp4, Sntb1, Hey2, Fabp7, Syne2, Hmgcs2, Vim, Lpar1, Lrrc58, Ahnak
Kctd12, Slc7a11, Apod, Clca3a1, Dcn, Phldb2, Bmp7, Yap1, Abca8a, Scd1
Negative: Ndrg4, Nsg2, Gad1, Eno2, Gng4, Dclk1, Calm2, Tubb2a, Napb, Aldoa.1
Vamp2, Atp2b1, Ncdn, Snap91, Ckb, Synpr, Pbx1, Meis2, Stx1b, Atp5b
Atp6v1e1, Stxbp1, Baiap2, Dlgap1, Mapk1, Cpne4, Sh3gl2, Dync1i1, Atp1a1, Map2k1
PC_ 2
Positive: Marcks, Apod, Plp1, Tpt1, Hmgcs2, Nr2f2, Ncam1, Cnn3, Sntb1, Kctd12
Scd1, Frzb, Sparc, Hey2, Fabp7, Lpar1, Igfbp4, Scd2, Kif5b, Mcf2l
2310022B05Rik, Ahnak, Phldb2, Igfbp5, Syne2, Omp, Nudt4, Trak2, Slc7a11, Clca3a1
Negative: Doc2g, Map1b, Plcxd2, Cdhr1, Map1a, Cck, Slc1a2, Eomes, Rab3b, Gabra1
Syt7, C230004F18Rik, Sept3, Gap43, Rcan2, Nefl, Arap2, Ankrd34c, Kitl, Fat3
Adarb1, Sncb, mt-Nd2, Cacnb4, Slc6a11, Myo5a, Ptprd, Nrsn1, Nptx1, Deptor
PC_ 3
Positive: Pde1c, Eomes, Nrsn1, Id3, Sparcl1, Msi2, Impact, Deptor, Neurod1, Ly6g6e
Pip5k1b, Cdhr1, Cck, S100a5, Nptx1, Slc17a6, Gucy1a1, Calb2, Gabra1, Grm1
Grem1, Zbtb20, Shisa9, Fabp7, Cacnb2, Ptn, Cacna2d2, Vsnl1, Adk, Spon1
Negative: C230004F18Rik, Camk2n1, Nrgn, Ptk2b, Camk4, Rasl10b, Luzp2, Pcp4, Penk, Icam5
Sez6, Rasa2, Kcnb2, Dgkb, Sema3c, Abl2, Nrep, Rbfox3, Rasgrp1, Ube2ql1
Kalrn, Ablim3, Eml5, Gng4, Slc1a2, Agap2, 2900052N01Rik, Map1a, Inpp5j, Prkca
PC_ 4
Positive: Nefm, Ankrd34c, Igfbp5, Gabra1, Rasd2, Kitl, Ptprd, Rab3b, Plcxd2, Mtor
Nudt4, Doc2g, Raver2, Kcna2, Atrnl1, Fat3, Dnajc6, Ralyl, Ndnf, Sema3c
Dcn, Elavl2, Igfbp7, Cdhr1, Plekha4, Jam2, Nptx1, Nefh, Dst, Fam171b
Negative: Gria1, Gpm6b, Nyap2, Slc1a3, Pde1c, Vsnl1, Slc6a11, Shisa9, Grem1, Nrsn1
Nap1l5, Aqp4, Zeb2, Nxph1, Magi1, Tcf4, Neurod1, H3f3b, Pip5k1b, Car2
Rcn2, Etv1, Gpm6a, Nrxn1, Serpine2, Ntrk2, Ly6g6e, Cacnb2, Celf4, Slc4a4
PC_ 5
Positive: Clca3a1, Ttyh1, Qk, Cntn1, Spred1, Prnp, Mcf2l, Abca8a, Tulp4, Kif5b
Mmd2, Rgcc, Omp, Smchd1, Smim10l1, Sntb1, Hey2, Kif2a, Tardbp, Calm3
Mprip, Ptprz1, Celf2, Ntrk2, Mindy2, Trak2, Frzb, Unc13c, Hmgcs2, Gsk3b
Negative: Ogn, Fn1, Hba-a2, Alcam, Hbb-bs, Hba-a1, Efemp1, Cfh, Dcn, Maf
Slc38a2, Cald1, Cldn11, Ahnak, Slc7a11, Macf1, Prrc2b, Bsg, Fth1, Atp1a2
Id3, Aqp4, Mdh1, Etv1, Agpat3, Slc17a6, Id2, Eif4g2, Cers6, Sh3bgrl
Computing nearest neighbor graph
Computing SNN
Quitting from lines 287-312 (spaniel-vignette.Rmd)
Error: processing vignette 'spaniel-vignette.Rmd' failed with diagnostics:
invalid class "Graph" object: superclass "Mnumeric" not defined in the environment of the object's class
--- failed re-building ‘spaniel-vignette.Rmd’
SUMMARY: processing the following file failed:
‘spaniel-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted