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BiocCheckGitClone('MBECS')
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This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
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R CMD CHECK
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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2497/fa3118da298cdcf75f96f4678e48596e18ddaf7e/MBECS.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'limma', 'lme4', 'lmerTest', 'pheatmap', 'rmarkdown', 'markdown',
'cluster', 'dplyr', 'ggplot2', 'gridExtra', 'ruv', 'sva', 'tibble',
'tidyr', 'vegan', 'knitr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [30s/30s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘cluster’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘knitr’ ‘limma’ ‘lme4’
‘lmerTest’ ‘markdown’ ‘methods’ ‘pheatmap’ ‘rmarkdown’ ‘ruv’ ‘sva’
‘tibble’ ‘tidyr’ ‘vegan’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [55s/68s] NOTE
mbecMixedVariance: no visible binding for global variable ‘.’
mbecModelVariancePVCA: no visible binding for global variable ‘.’
mbecMosaic: no visible binding for global variable ‘Freq’
mbecMosaicPlot: no visible binding for global variable ‘Var1’
mbecMosaicPlot: no visible binding for global variable ‘Freq.scaled’
mbecMosaicPlot: no visible binding for global variable ‘Var2’
mbecPVCAStatsPlot: no visible binding for global variable ‘type’
mbecPVCAStatsPlot: no visible binding for global variable ‘covariate’
mbecPVCAStatsPlot: no visible binding for global variable ‘variance’
mbecPVCAStatsPlot: no visible binding for global variable ‘variance.p’
mbecRDAStatsPlot: no visible binding for global variable ‘type’
mbecRDAStatsPlot: no visible binding for global variable ‘variance’
mbecRDAStatsPlot: no visible binding for global variable ‘covariate’
mbecRDAStatsPlot: no visible binding for global variable ‘variance.r’
mbecRLE: no visible binding for global variable ‘.’
mbecRLE: no visible binding for global variable ‘plot.order’
mbecRLE: no visible binding for global variable ‘specimen’
mbecRLEPlot: no visible binding for global variable ‘specimen’
mbecRLEPlot: no visible binding for global variable ‘values’
mbecSCOEFStatsPlot: no visible binding for global variable ‘variable’
mbecSCOEFStatsPlot: no visible binding for global variable ‘type’
mbecSCOEFStatsPlot: no visible binding for global variable
‘sil.coefficient’
mbecSCOEFStatsPlot: no visible binding for global variable ‘cluster’
mbecVarianceStatsLM: no visible binding for global variable ‘.’
mbecVarianceStatsPlot: no visible binding for global variable ‘type’
mbecVarianceStatsPlot: no visible binding for global variable
‘variance’
mbecVarianceStatsPlot: no visible binding for global variable
‘covariate’
Undefined global functions or variables:
. Freq Freq.scaled Var1 Var2 cluster covariate plot.order
sil.coefficient specimen type values variable variance variance.p
variance.r
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 14 mins
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BiocCheck('MBECS_0.99.8.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
[287s/515s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mbecReportPost 114.572 1.660 196.904
mbecReportPrelim 54.115 0.855 107.485
mbecModelVariance 16.716 0.417 27.917
mbecVarianceStatsPlot 14.981 0.380 33.085
mbecCorrection 5.216 0.123 9.091
percentileNorm 4.423 0.051 10.254
mbecRunCorrections 3.999 0.057 8.002
mbecBox 3.752 0.118 7.588
mbecBoxPlot 3.187 0.037 6.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2497/fa3118da298cdcf75f96f4678e48596e18ddaf7e/MBECS_0.99.8.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmplKDw7A/file16bf315debcfe/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Microarray, Metabolomics, Proteomics,
Epigenetics, Cheminformatics, Transcriptomics, Normalization,
Preprocessing, Bayesian, Clustering, Regression, ExonArray,
GeneExpression, RNASeq, OneChannel, TwoChannel, MicroRNAArray,
mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology,
ImmunoOncology, AlternativeSplicing, DifferentialExpression,
DifferentialSplicing, GeneSetEnrichment, MultipleComparison,
QualityControl, TimeCourse, DataImport
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MBECS...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressMessages() in R/mbecs_analyses.R (line 976, column 5)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 12 functions > 50 lines.
The longest 5 functions are:
mbecPCAPlot() (R/mbecs_plots.R, line 361): 187 lines
mbecReportPost() (R/mbecs_reports.R, line 138): 139 lines
mbecMosaicPlot() (R/mbecs_plots.R, line 239): 97 lines
mbecBoxPlot() (R/mbecs_plots.R, line 89): 90 lines
MbecData() (R/mbecs_classes.R, line 77): 82 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
pipe.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 9 lines (0%) are > 80 characters
long.
First 6 lines:
R/mbecs_corrections.R:571 tmp.mod <- stats::model.matrix( ~ tmp...
R/mbecs_helper.R:133 # fit lm to every feature with treatment a...
R/mbecs_plots.R:496 ...
vignettes/mbecs_vignette.Rmd:306 ```{r Usage_multiple_correction, echo=...
vignettes/mbecs_vignette.Rmd:479 ```{r Usage_varLM, echo=TRUE, eval=TRU...
vignettes/mbecs_vignette.Rmd:503 ```{r Usage_varLMM, echo=TRUE, eval=TR...
* NOTE: Consider multiples of 4 spaces for line indents, 667
lines(8%) are not.
First 6 lines:
R/mbecs_analyses.R:54 required.col=eval(model.va...
R/mbecs_analyses.R:55 label=label)
R/mbecs_analyses.R:82 by = "specimen")...
R/mbecs_analyses.R:84 get(mode...
R/mbecs_analyses.R:146 function(input.obj, model.vars = c("b...
R/mbecs_analyses.R:152 pca.axes=c(1,2), type="clr"...
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.