| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:30 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
To the developers/maintainers of the SCArray.sat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCArray.sat.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1802/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SCArray.sat 0.99.4 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: SCArray.sat |
| Version: 0.99.4 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SCArray.sat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SCArray.sat_0.99.4.tar.gz |
| StartedAt: 2023-04-11 23:16:44 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 23:21:49 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 305.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SCArray.sat.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SCArray.sat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SCArray.sat_0.99.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SCArray.sat.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SCArray.sat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCArray.sat’ version ‘0.99.4’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘Seurat:::FastExpMean’ ‘Seurat:::FastLogVMR’ ‘Seurat:::NBResiduals’
‘Seurat:::UpdateKey’
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
* 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 ...
‘SCArray.sat.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SCArray.sat.Rcheck/00check.log’
for details.
SCArray.sat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SCArray.sat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
Attaching package: 'sp'
The following object is masked from 'package:IRanges':
%over%
Calling scNewAssayGDS() ...
Input: /home/biocbuild/bbs-3.17-bioc/R/site-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
|
| | 0%
|
| | 1%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======= | 11%
|
|======== | 11%
|
|======== | 12%
|
|========= | 12%
|
|========= | 13%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 19%
|
|============== | 20%
|
|============== | 21%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 29%
|
|===================== | 30%
|
|===================== | 31%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 39%
|
|============================ | 40%
|
|============================ | 41%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 49%
|
|=================================== | 50%
|
|=================================== | 51%
|
|==================================== | 51%
|
|==================================== | 52%
|
|===================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|====================================== | 55%
|
|======================================= | 55%
|
|======================================= | 56%
|
|======================================== | 57%
|
|======================================== | 58%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 59%
|
|========================================== | 60%
|
|========================================== | 61%
|
|=========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================= | 65%
|
|============================================== | 65%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|=============================================== | 68%
|
|================================================ | 68%
|
|================================================ | 69%
|
|================================================= | 69%
|
|================================================= | 70%
|
|================================================= | 71%
|
|================================================== | 71%
|
|================================================== | 72%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|==================================================== | 75%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 77%
|
|====================================================== | 78%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 79%
|
|======================================================== | 80%
|
|======================================================== | 81%
|
|========================================================= | 81%
|
|========================================================= | 82%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 99%
|
|======================================================================| 100%
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 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%
|
| | 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%
RUNIT TEST PROTOCOL -- Tue Apr 11 23:21:15 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
30.055 1.434 31.478
SCArray.sat.Rcheck/SCArray.sat-Ex.timings
| name | user | system | elapsed | |
| CreateAssayObject2 | 0.107 | 0.000 | 0.107 | |
| NormalizeData | 0.960 | 0.056 | 1.015 | |
| RunPCA | 2.920 | 0.115 | 3.036 | |
| ScaleData | 1.548 | 0.045 | 1.593 | |
| scGetFiles | 0.381 | 0.032 | 0.414 | |
| scMemory | 1.761 | 0.159 | 1.920 | |
| scNewAssayGDS | 0.391 | 0.016 | 0.408 | |
| scNewSeuratGDS | 0.412 | 0.016 | 0.428 | |