Michael Olbrich
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MBECS |
| git_branch: RELEASE_3_17 |
| git_last_commit: 2b7aed2 |
| git_last_commit_date: 2023-04-25 11:36:23 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:05 -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 1136/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MBECS 1.4.0 (landing page) Michael Olbrich
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the MBECS 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: MBECS |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MBECS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MBECS_1.4.0.tar.gz |
| StartedAt: 2023-10-18 05:07:25 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 05:14:52 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 447.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MBECS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MBECS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MBECS_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MBECS.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 ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.4.0’
* 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 ‘MBECS’ 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 ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mbecModelVariance 7.644 0.100 11.381
mbecVarianceStatsPlot 7.151 0.094 10.944
mbecCorrection 6.298 0.217 10.023
mbecReportPost 4.321 0.082 6.370
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: OK
MBECS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MBECS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘MBECS’ ... ** using staged installation ** R ** data ** 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 (MBECS)
MBECS.Rcheck/tests/testthat.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.
> library(testthat)
> library(MBECS)
>
> test_check("MBECS")
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
No negative control features provided.
Using pseudo-negative controls.
Applying Remove Unwanted Variantion v3 (RUV-III).
No 'sID' column present, creating from rownames now.
No 'sID' column present, creating from rownames now.
Set tss-transformed counts.
No 'sID' column present, creating from rownames now.
Set tss-transformed counts.
Construct lm-formula from covariates.
Construct lm-formula from covariates.
There is a problem with the estimatibility of your model.
Check out covariate: 'sIDS40'
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Calculating RLE for group: A
Calculating RLE for group: B
Fitting linear model to every feature and extract proportion of
variance explained by covariates.
Construct formula from covariates.
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Fitting linear-mixed model to every feature and extract proportion
of variance explained by covariates.
Construct formula from covariates.
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boundary (singular) fit: see help('isSingular')
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[1] "batch"
[1] "group"
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
(1/#features) for log-ratio transformation.
Applying ComBat (sva) for batch-correction.
Found2batches
Adjusting for1covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding nonparametric adjustments
Adjusting the Data
[ FAIL 0 | WARN 101 | SKIP 0 | PASS 282 ]
[ FAIL 0 | WARN 101 | SKIP 0 | PASS 282 ]
>
> proc.time()
user system elapsed
79.840 1.931 124.585
MBECS.Rcheck/MBECS-Ex.timings
| name | user | system | elapsed | |
| MbecData | 0.111 | 0.007 | 0.184 | |
| colinScore | 0.389 | 0.027 | 0.641 | |
| dot-mbecGetData | 0.036 | 0.003 | 0.059 | |
| dot-mbecGetPhyloseq | 0.043 | 0.002 | 0.071 | |
| dot-mbecSetData | 0.047 | 0.003 | 0.076 | |
| dummy.list | 0.005 | 0.001 | 0.012 | |
| dummy.mbec | 0.026 | 0.002 | 0.046 | |
| dummy.ps | 0.005 | 0.001 | 0.011 | |
| mbecBox | 2.587 | 0.044 | 4.039 | |
| mbecBoxPlot | 2.287 | 0.025 | 3.553 | |
| mbecCorrection | 6.298 | 0.217 | 10.023 | |
| mbecDummy | 0.138 | 0.018 | 0.237 | |
| mbecGetData-MbecData-method | 0.034 | 0.004 | 0.057 | |
| mbecGetData | 0.033 | 0.004 | 0.055 | |
| mbecGetPhyloseq-MbecData-method | 0.054 | 0.005 | 0.090 | |
| mbecGetPhyloseq | 0.098 | 0.006 | 0.162 | |
| mbecHeat | 0.173 | 0.008 | 0.280 | |
| mbecHeatPlot | 0.147 | 0.008 | 0.239 | |
| mbecHelpFactor | 0.006 | 0.002 | 0.008 | |
| mbecLM | 1.080 | 0.036 | 1.706 | |
| mbecMixedVariance | 0.045 | 0.003 | 0.077 | |
| mbecModelVariance | 7.644 | 0.100 | 11.381 | |
| mbecMosaic | 1.015 | 0.015 | 1.585 | |
| mbecMosaicPlot | 0.894 | 0.013 | 1.334 | |
| mbecPCA-MbecData-method | 0.997 | 0.017 | 1.548 | |
| mbecPCA | 1.050 | 0.020 | 1.587 | |
| mbecPCAPlot | 0.923 | 0.017 | 1.434 | |
| mbecPVCAStatsPlot | 1.261 | 0.022 | 1.934 | |
| mbecProcessInput-MbecData-method | 0.029 | 0.003 | 0.040 | |
| mbecProcessInput-list-method | 0.029 | 0.003 | 0.041 | |
| mbecProcessInput-phyloseq-method | 0.039 | 0.002 | 0.058 | |
| mbecProcessInput | 0.028 | 0.003 | 0.048 | |
| mbecRDAStatsPlot | 0.121 | 0.005 | 0.195 | |
| mbecRLE | 0.249 | 0.008 | 0.388 | |
| mbecRLEPlot | 0.197 | 0.006 | 0.300 | |
| mbecReportPost | 4.321 | 0.082 | 6.370 | |
| mbecReportPrelim | 2.232 | 0.034 | 2.903 | |
| mbecRunCorrections | 2.200 | 0.046 | 2.855 | |
| mbecSCOEFStatsPlot | 0.071 | 0.003 | 0.097 | |
| mbecSetData-MbecData-method | 0.049 | 0.004 | 0.067 | |
| mbecSetData | 0.047 | 0.004 | 0.064 | |
| mbecTestModel | 0.034 | 0.003 | 0.047 | |
| mbecTransform | 0.232 | 0.009 | 0.311 | |
| mbecValidateModel | 0.036 | 0.003 | 0.051 | |
| mbecVarianceStats | 0.018 | 0.002 | 0.023 | |
| mbecVarianceStatsPlot | 7.151 | 0.094 | 10.944 | |
| percentileNorm | 2.029 | 0.030 | 3.170 | |
| poscore | 0.000 | 0.001 | 0.000 | |