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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1820/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCArray.sat 1.0.3  (landing page)
Xiuwen Zheng
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SCArray.sat
git_branch: RELEASE_3_17
git_last_commit: 9f3731f
git_last_commit_date: 2023-07-10 15:44:53 -0400 (Mon, 10 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for SCArray.sat on kjohnson2


To the developers/maintainers of the SCArray.sat package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SCArray.sat
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SCArray.sat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SCArray.sat_1.0.3.tar.gz
StartedAt: 2023-10-18 21:46:58 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 21:56:06 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 547.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SCArray.sat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SCArray.sat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SCArray.sat_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SCArray.sat.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCArray.sat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCArray.sat’ version ‘1.0.3’
* 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 ‘SCArray.sat’ 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:
  ‘Seurat:::DEmethods_counts’ ‘Seurat:::DEmethods_nocorrect’
  ‘Seurat:::FastExpMean’ ‘Seurat:::FastLogVMR’ ‘Seurat:::NBResiduals’
  ‘Seurat:::UpdateKey’ ‘Seurat:::ValidateDataForMerge’
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
RunPCA 3.148  0.116   5.801
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SCArray.sat.Rcheck/00check.log’
for details.



Installation output

SCArray.sat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SCArray.sat
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SCArray.sat’ ...
** using staged installation
** R
** 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 (SCArray.sat)

Tests output

SCArray.sat.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("SCArray.sat")

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


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


Attaching package: 'S4Vectors'

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

    expand, unname

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'S4Arrays'

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

    abind

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

    rowsum


Attaching package: 'DelayedArray'

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

    apply, scale, sweep

The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)

Attaching package: 'sp'

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

    %over%

Calling scNewAssayGDS() ...
Input: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SCArray/extdata/example.gds
    counts: 1000 x 850
Calling SCArray:::x_colSums() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calling SCArray:::x_colSums() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calling NormalizeData.SC_GDSMatrix() ...
Normalizing across features (CLR)
Calling SCArray:::x_rowSums() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Normalizing across features
Calling NormalizeData.SC_GDSMatrix() ...
Normalizing across cells (CLR)
Calling SCArray:::x_colSums() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Normalizing across cells
Calling NormalizeData.SC_GDSMatrix() ...
Performing relative-counts-normalization
Calling SCArray:::x_colSums() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Performing relative-counts-normalization
Calling NormalizeData.SC_GDSMatrix() ...
Performing log-normalization
Calling SCArray:::x_colSums() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calling FindVariableFeatures.SC_GDSMatrix() ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calling FindVariableFeatures.SC_GDSMatrix() ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calling FindVariableFeatures.SC_GDSMatrix() ...
Calculating gene variances
Calling SCArray::scRowMeanVar() with SC_GDSMatrix [1000x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calculating feature variances of standardized and clipped values

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calling ScaleData.SC_GDSMatrix() with SC_GDSMatrix [1000x850] ...
Regressing out: x1, x2
Writing to '_temp_scale_data.gds'
Calling SCArray::row_nnzero() with SC_GDSMatrix [500x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Centering and scaling data matrix (SC_GDSMatrix [500x850])
Writing to '_scale_data.gds'
Calling SCArray::scRowMeanVar() with transposed SC_GDSMatrix [500x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Delete '_temp_scale_data.gds'
Regressing out x1, x2

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Centering and scaling data matrix

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  |======================================================================| 100%
Calling ScaleData.SC_GDSMatrix() with SC_GDSMatrix [1000x850] ...
Centering and scaling data matrix (SC_GDSMatrix [500x850])
Writing to '_scale_data2.gds'
Data split (SC_GDSMatrix [500,425]): FALSE
Calling SCArray::scRowMeanVar() with SC_GDSMatrix [500x425] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%

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  |================================================================| 100%
Data split (SC_GDSMatrix [500,425]): TRUE
Calling SCArray::scRowMeanVar() with SC_GDSMatrix [500x425] ...

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  |                                                                |   0%
  |                                                                      
  |================================================================| 100%

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  |================================================================| 100%
Centering and scaling data matrix
Centering and scaling data from split FALSE

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  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Centering and scaling data from split TRUE

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  |======================================================================| 100%
Calling ScaleData.SC_GDSMatrix() with SC_GDSMatrix [1000x850] ...
Centering and scaling data matrix (SC_GDSMatrix [500x850])
Calling SCArray::scRowMeanVar() with SC_GDSMatrix [500x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Centering and scaling data matrix

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  |======================================================================| 100%
Calling RunPCA.SCArrayAssay() ...
Calling RunPCA.SC_GDSMatrix() with SC_GDSMatrix [500x850] ...
Calling SCArray:::x_rowVars() with SC_GDSMatrix [500x850] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calling SCArray:::x_crossprod_x() with transposed SC_GDSMatrix [850x500] ...

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%
Calling SCArray:::x_multiply_x_yANY() with transposed SC_GDSMatrix [850x500] ...


RUNIT TEST PROTOCOL -- Wed Oct 18 21:55:43 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SCArray.sat RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 30.381   1.447  56.623 

Example timings

SCArray.sat.Rcheck/SCArray.sat-Ex.timings

nameusersystemelapsed
CreateAssayObject20.1120.0050.207
NormalizeData1.8620.0463.769
RunPCA3.1480.1165.801
ScaleData1.8560.0783.469
scGetFiles0.4440.0190.830
scMemory1.0290.0531.929
scNewAssayGDS1.1610.0342.130
scNewSeuratGDS0.4930.0180.914