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CHECK report for phemd on tokay1

This page was generated on 2021-05-06 12:32:45 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the phemd package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1336/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phemd 1.6.0  (landing page)
William S Chen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/phemd
Branch: RELEASE_3_12
Last Commit: cc357fc
Last Changed Date: 2020-10-27 11:42:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: phemd
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phemd.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings phemd_1.6.0.tar.gz
StartedAt: 2021-05-06 05:30:27 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:37:54 -0400 (Thu, 06 May 2021)
EllapsedTime: 447.0 seconds
RetCode: 1
Status:   ERROR   
CheckDir: phemd.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phemd.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings phemd_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/phemd.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 '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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/phemd.Rcheck/00check.log'
for details.


Installation output

phemd.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/phemd_1.6.0.tar.gz && rm -rf phemd.buildbin-libdir && mkdir phemd.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phemd.buildbin-libdir phemd_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL phemd_1.6.0.zip && rm phemd_1.6.0.tar.gz phemd_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  479k  100  479k    0     0  13.1M      0 --:--:-- --:--:-- --:--:-- 13.3M

install for i386

* installing *source* package 'phemd' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'phemd'
    finding HTML links ... done
    GDM                                     html  
    Phemd-methods                           html  
    Phemd                                   html  
    aggregateSamples                        html  
    all_expn_data                           html  
    all_genes                               html  
    assignCellClusterNearestNode            html  
    batchIDs                                html  
    bindSeuratObj                           html  
    celltypeFreqs                           html  
    clusterIndividualSamples                html  
    compareSamples                          html  
    createDataObj                           html  
    drawColnames45                          html  
    embedCells                              html  
    gaussianffLocal                         html  
    generateGDM                             html  
    getArithmeticCentroids                  html  
    getCellYield                            html  
    getSampleCelltypeFreqs                  html  
    getSampleHistsByCluster                 html  
    getSampleSizes                          html  
    groupSamples                            html  
    heatmap_genes                           html  
    identifyCentroids                       html  
    monocleInfo                             html  
    orderCellsMonocle                       html  
    phateInfo                               html  
    plotCellYield                           html  
    plotEmbeddings                          html  
    plotGroupedSamplesDmap                  html  
    plotHeatmaps                            html  
    plotSummaryHistograms                   html  
    pooledCells                             html  
    printClusterAssignments                 html  
    rawExpn                                 html  
    removeTinySamples                       html  
    retrieveRefClusters                     html  
    sNames                                  html  
    selectFeatures                          html  
    selectMarkers                           html  
    selected_genes                          html  
    seuratInfo                              html  
    snames_data                             html  
    subsampledBool                          html  
    subsampledIdx                           html  
** 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

install for x64

* installing *source* package 'phemd' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phemd' as phemd_1.6.0.zip
* DONE (phemd)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'phemd' successfully unpacked and MD5 sums checked

Tests output


Example timings

phemd.Rcheck/examples_i386/phemd-Ex.timings

nameusersystemelapsed
GDM1.80.01.8
Phemd-methods11.00 0.8511.86
aggregateSamples1.790.021.81
assignCellClusterNearestNode000
batchIDs0.570.000.57

phemd.Rcheck/examples_x64/phemd-Ex.timings

nameusersystemelapsed
GDM0.910.000.91
Phemd-methods14.91 0.0714.98
aggregateSamples3.160.023.17
assignCellClusterNearestNode000
batchIDs0.670.000.67