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) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 1820/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SCArray.sat 1.0.3 (landing page) Xiuwen Zheng
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
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. |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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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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%
|
| | 0%
|
|================================================================| 100%
Data split (SC_GDSMatrix [500,425]): TRUE
Calling SCArray::scRowMeanVar() with SC_GDSMatrix [500x425] ...
|
| | 0%
|
|================================================================| 100%
|
| | 0%
|
|================================================================| 100%
Centering and scaling data matrix
Centering and scaling data from split FALSE
|
| | 0%
|
|======================================================================| 100%
Centering and scaling data from split TRUE
|
| | 0%
|
|======================================================================| 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
|
| | 0%
|
|======================================================================| 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
SCArray.sat.Rcheck/SCArray.sat-Ex.timings
| name | user | system | elapsed | |
| CreateAssayObject2 | 0.112 | 0.005 | 0.207 | |
| NormalizeData | 1.862 | 0.046 | 3.769 | |
| RunPCA | 3.148 | 0.116 | 5.801 | |
| ScaleData | 1.856 | 0.078 | 3.469 | |
| scGetFiles | 0.444 | 0.019 | 0.830 | |
| scMemory | 1.029 | 0.053 | 1.929 | |
| scNewAssayGDS | 1.161 | 0.034 | 2.130 | |
| scNewSeuratGDS | 0.493 | 0.018 | 0.914 | |