nebbiolo1 Summary
[top]
Package: MBECS |
Version: 0.99.9 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MBECS |
BuildTime: 0 minutes 49.13 seconds |
CheckCommand: BiocCheckGitClone('MBECS') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings MBECS_0.99.9.tar.gz && BiocCheck('MBECS_0.99.9.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 51.24 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 455.28 KiB |
BuildID:: MBECS_20220217163937 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MBECS. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* preparing ‘MBECS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘MBECS_0.99.9.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('MBECS')
===============================
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
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2497/1f868cfed1f7e0e4871ba131b2425fd6b6a196be/MBECS.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘0.99.9’
* 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 ... [19s/19s] 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 ... [18s/18s] 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 ... [0s/0s] 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 ... [43s/43s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [288s/289s]
[289s/289s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2497/1f868cfed1f7e0e4871ba131b2425fd6b6a196be/MBECS.Rcheck/00check.log’
for details.
===============================
BiocCheck('MBECS_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2497/1f868cfed1f7e0e4871ba131b2425fd6b6a196be/MBECS_0.99.9.tar.gz" "/tmp/RtmpWypKM9/file2d5453a08af55/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 122): 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:
mbecReportPost.Rd, mbecReportPrelim.Rd, 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.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
Package: MBECS |
Version: 0.99.9 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MBECS |
BuildTime: 1 minutes 9.01 seconds |
CheckCommand: BiocCheckGitClone('MBECS') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MBECS_0.99.9.tar.gz && BiocCheck('MBECS_0.99.9.tar.gz', `new-package`=TRUE) |
CheckTime: 11 minutes 19.34 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MBECS_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 25.72 seconds |
PackageFileSize: 452.57 KiB |
BuildID:: MBECS_20220217163937 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MBECS. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* preparing ‘MBECS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘MBECS_0.99.9.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('MBECS')
===============================
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
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2497/1f868cfed1f7e0e4871ba131b2425fd6b6a196be/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 ‘0.99.9’
* 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 ... [26s/26s] 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 ... [25s/26s] 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 ... [0s/0s] 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 ... [54s/54s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mbecModelVariance 6.913 0.140 7.053
mbecVarianceStatsPlot 6.252 0.138 6.390
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [424s/424s]
[424s/424s] 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: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2497/1f868cfed1f7e0e4871ba131b2425fd6b6a196be/MBECS.Rcheck/00check.log’
for details.
===============================
BiocCheck('MBECS_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* 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/2497/1f868cfed1f7e0e4871ba131b2425fd6b6a196be/MBECS_0.99.9.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp15T5MI/file49b9340b1d21/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 122): 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:
mbecReportPost.Rd, mbecReportPrelim.Rd, 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
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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
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https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
merida1 BUILD BIN output
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R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MBECS_0.99.9.tar.gz'
>>>>>>>
* 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)