| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:12 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1097/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MBECS 1.3.1 (landing page) Michael Olbrich
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| 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/library --timings MBECS_1.3.1.tar.gz |
| StartedAt: 2023-02-07 07:01:33 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 07:08:24 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 410.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MBECS.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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/library --timings MBECS_1.3.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MBECS.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘ConQuR’ ‘caret’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
externalPLSDA: no visible global function definition for ‘mbecsDeflate’
mbecExplainedVariance: no visible global function definition for
‘setNames’
mbecPLSDA: no visible global function definition for ‘helpFactor’
mbecPLSDA: no visible global function definition for ‘model.matrix’
mbecPLSDA: no visible binding for global variable ‘.’
mbecPLSDA: no visible binding for global variable ‘Freq’
mbecPLSDA: no visible binding for global variable ‘weight’
mbecPLSDA: no visible global function definition for ‘mbecsDeflate’
Undefined global functions or variables:
. Freq helpFactor mbecsDeflate model.matrix setNames weight
Consider adding
importFrom("stats", "model.matrix", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'mbecCorrection':
mbecCorrection
Code: function(input.obj, model.vars = c("batch", "group"), method =
c("lm", "lmm", "sva", "ruv2", "ruv4", "ruv3", "bmc",
"bat", "rbe", "pn", "svd", "pls"), type = c("clr",
"otu", "tss"), nc.features = NULL)
Docs: function(input.obj, model.vars = c("batch", "group"), method =
c("lm", "lmm", "sva", "ruv2", "ruv4", "ruv3", "bmc",
"bat", "rbe", "pn", "svd"), type = c("clr", "otu",
"tss"), nc.features = NULL)
Mismatches in argument default values:
Name: 'method'
Code: c("lm", "lmm", "sva", "ruv2", "ruv4", "ruv3", "bmc", "bat", "rbe",
"pn", "svd", "pls")
Docs: c("lm", "lmm", "sva", "ruv2", "ruv4", "ruv3", "bmc", "bat", "rbe",
"pn", "svd")
Codoc mismatches from documentation object 'mbecRunCorrections':
mbecRunCorrections
Code: function(input.obj, model.vars = c("batch", "group"), type =
"clr", method = c("ruv3", "bmc", "bat", "rbe", "pn",
"svd", "pls"), nc.features = NULL)
Docs: function(input.obj, model.vars = c("batch", "group"), type =
"clr", method = c("ruv3", "bmc", "bat", "rbe", "pn",
"svd"), nc.features = NULL)
Mismatches in argument default values:
Name: 'method' Code: c("ruv3", "bmc", "bat", "rbe", "pn", "svd", "pls") Docs: c("ruv3", "bmc", "bat", "rbe", "pn", "svd")
* 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 20.855 0.480 22.597
mbecVarianceStatsPlot 18.862 0.092 19.063
mbecCorrection 7.519 0.089 7.684
mbecReportPost 5.622 0.092 5.785
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-corrections.R:203'): mbecPLSDA works ───────────────────────────
Error in `helpFactor(tmp.meta, model.vars)`: could not find function "helpFactor"
Backtrace:
▆
1. ├─testthat::evaluate_promise(...) at test-corrections.R:203:4
2. │ ├─withr::with_output_sink(...)
3. │ │ └─base::force(code)
4. │ ├─base::withCallingHandlers(...)
5. │ └─base::withVisible(code)
6. └─MBECS:::mbecPLSDA(input.obj = dummy.mbec, model.vars, type = "otu")
[ FAIL 1 | WARN 101 | SKIP 4 | PASS 265 ]
Error: Test failures
Execution halted
* 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 ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘mbecs_vignette.Rmd’ using knitr
Killed
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MBECS.Rcheck/00check.log’
for details.
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/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.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
Applying PLSDA for batch-correction.
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'
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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[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 1 | WARN 101 | SKIP 4 | PASS 265 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (4)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-corrections.R:203'): mbecPLSDA works ───────────────────────────
Error in `helpFactor(tmp.meta, model.vars)`: could not find function "helpFactor"
Backtrace:
▆
1. ├─testthat::evaluate_promise(...) at test-corrections.R:203:4
2. │ ├─withr::with_output_sink(...)
3. │ │ └─base::force(code)
4. │ ├─base::withCallingHandlers(...)
5. │ └─base::withVisible(code)
6. └─MBECS:::mbecPLSDA(input.obj = dummy.mbec, model.vars, type = "otu")
[ FAIL 1 | WARN 101 | SKIP 4 | PASS 265 ]
Error: Test failures
Execution halted
MBECS.Rcheck/MBECS-Ex.timings
| name | user | system | elapsed | |
| MbecData | 0.115 | 0.107 | 0.369 | |
| colinScore | 0.500 | 0.023 | 0.570 | |
| dot-mbecGetData | 0.035 | 0.003 | 0.039 | |
| dot-mbecGetPhyloseq | 0.047 | 0.000 | 0.047 | |
| dot-mbecSetData | 0.054 | 0.000 | 0.054 | |
| dummy.list | 0.002 | 0.003 | 0.006 | |
| dummy.mbec | 0.026 | 0.000 | 0.026 | |
| dummy.ps | 0.005 | 0.000 | 0.006 | |
| mbecBox | 3.493 | 0.056 | 3.577 | |
| mbecBoxPlot | 2.712 | 0.000 | 2.712 | |
| mbecCorrection | 7.519 | 0.089 | 7.684 | |
| mbecDummy | 0.188 | 0.020 | 0.207 | |
| mbecGetData-MbecData-method | 0.031 | 0.004 | 0.035 | |
| mbecGetData | 0.031 | 0.003 | 0.035 | |
| mbecGetPhyloseq-MbecData-method | 0.048 | 0.005 | 0.053 | |
| mbecGetPhyloseq | 0.086 | 0.008 | 0.094 | |
| mbecHeat | 0.215 | 0.008 | 0.227 | |
| mbecHeatPlot | 0.184 | 0.004 | 0.188 | |
| mbecLM | 1.180 | 0.004 | 1.186 | |
| mbecMixedVariance | 0.051 | 0.000 | 0.050 | |
| mbecModelVariance | 20.855 | 0.480 | 22.597 | |
| mbecMosaic | 1.200 | 0.004 | 1.209 | |
| mbecMosaicPlot | 1.082 | 0.000 | 1.084 | |
| mbecPCA-MbecData-method | 1.153 | 0.008 | 1.163 | |
| mbecPCA | 1.169 | 0.000 | 1.169 | |
| mbecPCAPlot | 0.967 | 0.000 | 0.968 | |
| mbecPVCAStatsPlot | 1.411 | 0.004 | 1.426 | |
| mbecProcessInput-MbecData-method | 0.029 | 0.000 | 0.029 | |
| mbecProcessInput-list-method | 0.028 | 0.000 | 0.028 | |
| mbecProcessInput-phyloseq-method | 0.038 | 0.000 | 0.038 | |
| mbecProcessInput | 0.028 | 0.000 | 0.028 | |
| mbecRDAStatsPlot | 0.184 | 0.004 | 0.187 | |
| mbecRLE | 0.306 | 0.004 | 0.310 | |
| mbecRLEPlot | 0.203 | 0.008 | 0.211 | |
| mbecReportPost | 5.622 | 0.092 | 5.785 | |
| mbecReportPrelim | 2.829 | 0.008 | 2.838 | |
| mbecRunCorrections | 3.596 | 0.004 | 3.601 | |
| mbecSCOEFStatsPlot | 0.111 | 0.012 | 0.125 | |
| mbecSetData-MbecData-method | 0.055 | 0.000 | 0.054 | |
| mbecSetData | 0.053 | 0.000 | 0.053 | |
| mbecTestModel | 0.034 | 0.000 | 0.034 | |
| mbecTransform | 0.196 | 0.000 | 0.196 | |
| mbecValidateModel | 0.039 | 0.000 | 0.040 | |
| mbecVarianceStats | 0.042 | 0.000 | 0.042 | |
| mbecVarianceStatsPlot | 18.862 | 0.092 | 19.063 | |
| percentileNorm | 2.350 | 0.024 | 2.375 | |
| poscore | 0.000 | 0.000 | 0.001 | |