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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phemd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phemd_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/phemd.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phemd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phemd’ version ‘1.6.0’
* 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 ‘phemd’ can be installed ... OK
* 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 ... NOTE
Unexported objects imported by ':::' calls:
‘VGAM:::VGAM.weights.function’ ‘pheatmap:::find_coordinates’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ‘phemd-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bindSeuratObj
> ### Title: Attach 'Seurat' object to 'Phemd' object
> ### Aliases: bindSeuratObj
>
> ### ** Examples
>
>
> my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data))
> my_seuratObj <- Seurat::CreateSeuratObject(counts = t(all_expn_data[[1]]), project = "A")
> my_seuratObj <- Seurat::FindVariableFeatures(object = my_seuratObj)
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> my_seuratObj <- Seurat::ScaleData(object = my_seuratObj, do.scale=FALSE, do.center=FALSE)
|
| | 0%
|
|======================================================================| 100%
> my_seuratObj <- Seurat::RunPCA(object = my_seuratObj, pc.genes = colnames(all_expn_data[[1]]), do.print = FALSE)
Warning in irlba(A = t(x = object), nv = npcs, ...) :
You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1
Positive: SDR16C5, HSD11B1, CCDC173, PRDM5, TMEM63C, PRTG, PPIAL4E, SSTR5, CD19, CBR3-AS1
VWA1, ZNF695, PTGDR2, HES1, CCNE2, TMEM51-AS1, COL6A3, DCN, ZNF358, PLAC4
FAP, LOC644554, THY1, COL6A1, CD79A, TMEM150A, COL1A2, CDH5, ZNF671, COL1A1
Negative: S100A4, CD3D, CD2, SELL, TAP1, CD3G, CD3E, TNFRSF1B, DEF6, CD4
CD27, CALCOCO2, HAVCR2, FCGR3A, TIGIT, CCR7, TNFRSF9, CD8A, TCF7, DAXX
IL2RA, PECAM1, IFNG, PDCD1, TMEM183B, LETMD1, CD79B, CIITA, HMBOX1, ZCCHC11
PC_ 2
Positive: FCGR3A, CD14, CSF1R, CD163, S100A4, HAVCR2, PECAM1, CIITA, CD4, TMEM183B
TNFRSF1B, TARBP2, COL1A1, TAP1, FCGR3B, COL6A2, COL1A2, CALCOCO2, VWF, SELL
DAXX, COL6A1, CDH5, KCTD9, THY1, HMBOX1, COL6A3, CTNS, TMEM150A, CD79B
Negative: CD3D, CD2, CD3E, CD27, CD3G, CCR7, TIGIT, CD8A, PDCD1, DEF6
TCF7, LEF1, IL2RA, FOXP3, CTLA4, LAG3, IFNG, CCR8, CENPC1, ZNF749
LETMD1, TMEM51-AS1, TNFRSF9, CCNE2, ZNF671, ZNF695, PPIAL4E, TMEM63C, SSTR5, MFSD4
PC_ 3
Positive: FCGR3A, CD4, CD14, CSF1R, SELL, CD163, TNFRSF1B, CD79B, CIITA, IL2RA
TAP1, DEF6, FCGR3B, FOXP3, CCR7, CCR8, TIGIT, CD27, CTLA4, HAVCR2
BLK, FLJ34208, LACTB2, CD19, ZNF671, ZNF695, TCF7, SDR16C5, PRTG, HSD11B1
Negative: COL1A2, COL1A1, COL6A2, COL6A1, DCN, COL6A3, THY1, CALCOCO2, DAXX, FAP
VWF, TARBP2, S100A4, RNPEP, CDH5, NFATC1, KCTD9, ZNF358, TMEM150A, PECAM1
HMBOX1, ZCCHC11, CD3E, LETMD1, VWA1, CBR3-AS1, TMEM183B, CTNS, HES1, CD2
PC_ 4
Positive: CD4, CD27, CCR7, TNFRSF1B, IL2RA, CD79B, LETMD1, VWF, SELL, FOXP3
CDH5, CIITA, CCR8, TCF7, LEF1, PECAM1, CTLA4, TNFRSF9, TAP1, CD14
CSF1R, COL6A2, CALCOCO2, FAP, TIGIT, THY1, CTNS, TARBP2, VWA1, COL1A2
Negative: CD8A, FCGR3A, IFNG, S100A4, CD3E, CD3G, CD3D, DAXX, HMBOX1, TMEM183B
LAG3, HAVCR2, NCAM1, ZCCHC11, RNPEP, CD2, KCTD9, GJD4, ZNF671, CCNE2
TMEM51-AS1, CD79A, TMEM63C, SSTR5, SDR16C5, FCGR3B, LOC644554, CCDC173, PRDM5, HSD11B1
PC_ 5
Positive: S100A4, CD4, DEF6, TIGIT, CD14, CD3E, CD27, CD2, CD79B, PDCD1
CCR8, FOXP3, CTLA4, IL2RA, CSF1R, CD163, COL1A1, COL1A2, CALCOCO2, COL6A1
COL6A3, DCN, TNFRSF9, HAVCR2, RNPEP, TMEM51-AS1, NCAM1, NFATC1, ZNF358, ZNF695
Negative: SELL, CD8A, TAP1, VWF, PECAM1, CDH5, CCR7, LETMD1, CIITA, IFNG
VWA1, HMBOX1, BLK, TMEM150A, COL6A2, FAP, TMEM183B, CD3G, TNFRSF1B, TCF7
LEF1, ZCCHC11, FAM20B, THY1, CTNS, HES1, LACTB2, TARBP2, PLAC4, ZNF671
> my_seuratObj <- Seurat::FindNeighbors(my_seuratObj, reduction = "pca", dims.use = 1:10)
Warning: The following arguments are not used: dims.use
Suggested parameter: dims instead of dims.use
Warning: The following arguments are not used: dims.use
Suggested parameter: dims instead of dims.use
Computing nearest neighbor graph
Computing SNN
Error in validObject(.Object) :
invalid class “Graph” object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: <Anonymous> ... initialize -> callNextMethod -> .nextMethod -> validObject
Execution halted
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/phemd.Rcheck/00check.log’
for details.