| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:26 -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 MBECS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MBECS.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 1126/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MBECS 1.3.1 (landing page) Michael Olbrich
| 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: MBECS |
| Version: 1.3.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MBECS_1.3.1.tar.gz |
| StartedAt: 2023-04-11 21:20:07 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 21:25:10 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 303.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MBECS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MBECS_1.3.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MBECS.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 ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.3.1’
* 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 loading without being on the library search path ... 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
mbecCorrection 6.507 0.208 6.715
mbecModelVariance 6.176 0.048 6.224
mbecVarianceStatsPlot 5.937 0.020 5.957
* 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 ...
‘mbecs_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
MBECS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MBECS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.0 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.
> 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.
|
| | 0%
|
|==== | 5%
|
|======== | 10%
|
|============ | 15%
|
|================ | 20%
|
|==================== | 25%
|
|======================== | 30%
|
|============================ | 35%
|
|================================ | 40%
|
|==================================== | 45%
|
|======================================== | 50%
|
|============================================ | 55%
|
|================================================ | 60%
|
|==================================================== | 65%
|
|======================================================== | 70%
|
|============================================================ | 75%
|
|================================================================ | 80%
|
|==================================================================== | 85%
|
|======================================================================== | 90%
|
|============================================================================ | 95%
|
|================================================================================| 100%
Fitting linear-mixed model to every feature and extract proportion
of variance explained by covariates.
Construct formula from covariates.
|
| | 0%boundary (singular) fit: see help('isSingular')
|
|==== | 5%boundary (singular) fit: see help('isSingular')
|
|======== | 10%
|
|============ | 15%boundary (singular) fit: see help('isSingular')
|
|================ | 20%
|
|==================== | 25%
|
|======================== | 30%boundary (singular) fit: see help('isSingular')
|
|============================ | 35%
|
|================================ | 40%
|
|==================================== | 45%boundary (singular) fit: see help('isSingular')
|
|======================================== | 50%boundary (singular) fit: see help('isSingular')
|
|============================================ | 55%boundary (singular) fit: see help('isSingular')
|
|================================================ | 60%boundary (singular) fit: see help('isSingular')
|
|==================================================== | 65%boundary (singular) fit: see help('isSingular')
|
|======================================================== | 70%boundary (singular) fit: see help('isSingular')
|
|============================================================ | 75%boundary (singular) fit: see help('isSingular')
|
|================================================================ | 80%boundary (singular) fit: see help('isSingular')
|
|==================================================================== | 85%
|
|======================================================================== | 90%boundary (singular) fit: see help('isSingular')
|
|============================================================================ | 95%boundary (singular) fit: see help('isSingular')
|
|================================================================================| 100%
|
| | 0%
|
|======================================== | 50%
|
|================================================================================| 100%
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
[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
65.376 1.041 66.408
MBECS.Rcheck/MBECS-Ex.timings
| name | user | system | elapsed | |
| MbecData | 0.114 | 0.005 | 0.118 | |
| colinScore | 0.999 | 0.032 | 1.032 | |
| dot-mbecGetData | 0.034 | 0.000 | 0.034 | |
| dot-mbecGetPhyloseq | 0.04 | 0.00 | 0.04 | |
| dot-mbecSetData | 0.044 | 0.000 | 0.044 | |
| dummy.list | 0.005 | 0.000 | 0.005 | |
| dummy.mbec | 0.020 | 0.004 | 0.024 | |
| dummy.ps | 0.001 | 0.003 | 0.005 | |
| mbecBox | 2.229 | 0.092 | 2.321 | |
| mbecBoxPlot | 2.016 | 0.004 | 2.020 | |
| mbecCorrection | 6.507 | 0.208 | 6.715 | |
| mbecDummy | 0.108 | 0.000 | 0.108 | |
| mbecGetData-MbecData-method | 0.03 | 0.00 | 0.03 | |
| mbecGetData | 0.029 | 0.000 | 0.029 | |
| mbecGetPhyloseq-MbecData-method | 0.042 | 0.000 | 0.042 | |
| mbecGetPhyloseq | 0.039 | 0.000 | 0.039 | |
| mbecHeat | 0.182 | 0.000 | 0.182 | |
| mbecHeatPlot | 0.122 | 0.000 | 0.122 | |
| mbecHelpFactor | 0.005 | 0.000 | 0.005 | |
| mbecLM | 0.775 | 0.000 | 0.775 | |
| mbecMixedVariance | 0.034 | 0.003 | 0.038 | |
| mbecModelVariance | 6.176 | 0.048 | 6.224 | |
| mbecMosaic | 0.860 | 0.000 | 0.861 | |
| mbecMosaicPlot | 0.822 | 0.000 | 0.823 | |
| mbecPCA-MbecData-method | 0.921 | 0.024 | 0.944 | |
| mbecPCA | 0.869 | 0.019 | 0.889 | |
| mbecPCAPlot | 0.722 | 0.009 | 0.730 | |
| mbecPVCAStatsPlot | 0.923 | 0.004 | 0.927 | |
| mbecProcessInput-MbecData-method | 0.022 | 0.003 | 0.025 | |
| mbecProcessInput-list-method | 0.024 | 0.000 | 0.025 | |
| mbecProcessInput-phyloseq-method | 0.028 | 0.000 | 0.028 | |
| mbecProcessInput | 0.020 | 0.004 | 0.025 | |
| mbecRDAStatsPlot | 0.100 | 0.003 | 0.105 | |
| mbecRLE | 0.292 | 0.000 | 0.292 | |
| mbecRLEPlot | 0.116 | 0.000 | 0.116 | |
| mbecReportPost | 3.417 | 0.039 | 3.458 | |
| mbecReportPrelim | 1.727 | 0.000 | 1.727 | |
| mbecRunCorrections | 1.930 | 0.044 | 1.973 | |
| mbecSCOEFStatsPlot | 0.060 | 0.000 | 0.061 | |
| mbecSetData-MbecData-method | 0.043 | 0.000 | 0.043 | |
| mbecSetData | 0.043 | 0.000 | 0.042 | |
| mbecTestModel | 0.029 | 0.004 | 0.032 | |
| mbecTransform | 0.179 | 0.000 | 0.178 | |
| mbecValidateModel | 0.027 | 0.004 | 0.031 | |
| mbecVarianceStats | 0.013 | 0.004 | 0.018 | |
| mbecVarianceStatsPlot | 5.937 | 0.020 | 5.957 | |
| percentileNorm | 1.594 | 0.008 | 1.602 | |
| poscore | 0.001 | 0.000 | 0.000 | |