nebbiolo1 Summary
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| Package: EpiMix |
| Version: 0.99.5 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix |
| BuildTime: 6 minutes 26.63 seconds |
| CheckCommand: BiocCheckGitClone('EpiMix') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings EpiMix_0.99.5.tar.gz && BiocCheck('EpiMix_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 38.67 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2731.05 KiB |
| BuildID:: EpiMix_20220425233907 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EpiMix. 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: 0. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘EpiMix_0.99.5.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('EpiMix')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: EpiMix
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* this is package ‘EpiMix’ version ‘0.99.5’
* 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 ‘EpiMix’ can be installed ... [43s/43s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [41s/41s] NOTE
getLncRNAData: no visible global function definition for ‘query’
Undefined global functions or variables:
query
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GEO_Download_DNAMethylation.Rd':
\examples lines wider than 100 characters:
# METdirectories <- GEO_Download_DNAMethylation(AccessionID = "GSE114134", targetDirectory = tempdir())
Rd file 'TCGA_Preprocess_GeneExpression.Rd':
\examples lines wider than 100 characters:
# GEProcessedData <- TCGA_Preprocess_GeneExpression(CancerSite = "OV", MAdirectories = GEdirectories)
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [116s/165s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
EpiMix 26.303 1.743 28.634
EpiMix_PlotGene 15.793 1.219 37.168
EpiMix_PlotProbe 10.835 0.933 31.468
TCGA_Preprocess_DNAmethylation 4.980 2.370 8.788
TCGA_Download_DNAmethylation 4.993 2.269 9.167
GEO_Preprocess_DNAMethylation 5.848 0.617 6.956
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
* 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/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix.Rcheck/00check.log’
for details.
===============================
BiocCheck('EpiMix_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: EpiMix
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpYaFRyc/file3ed74a3d237159/EpiMix
─ installDir: /tmp/RtmpYaFRyc/file3ed74a2bf8c77c
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
* 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 4.1.0 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:
Preprocessing
Search 'biocViews' at https://contributions.bioconductor.org
* 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 for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of EpiMix...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/overview.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 24
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 27
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
TCGA_GetData.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.1% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1565 lines (15%) are > 80
characters long.
* NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 2925 lines
(29%) are not.
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...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 19 NOTES
See the EpiMix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: EpiMix |
| Version: 0.99.5 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix |
| BuildTime: 12 minutes 45.78 seconds |
| CheckCommand: BiocCheckGitClone('EpiMix') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EpiMix_0.99.5.tar.gz && BiocCheck('EpiMix_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.96 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh EpiMix_0.99.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 42.35 seconds |
| PackageFileSize: 2721.24 KiB |
| BuildID:: EpiMix_20220425233907 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EpiMix. 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: -9. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘EpiMix_0.99.5.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('EpiMix')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: EpiMix
─ PackageVersion: 0.99.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* this is package ‘EpiMix’ version ‘0.99.5’
* 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 ‘EpiMix’ can be installed ... [84s/100s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [95s/118s] NOTE
getLncRNAData: no visible global function definition for ‘query’
Undefined global functions or variables:
query
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GEO_Download_DNAMethylation.Rd':
\examples lines wider than 100 characters:
# METdirectories <- GEO_Download_DNAMethylation(AccessionID = "GSE114134", targetDirectory = tempdir())
Rd file 'TCGA_Preprocess_GeneExpression.Rd':
\examples lines wider than 100 characters:
# GEProcessedData <- TCGA_Preprocess_GeneExpression(CancerSite = "OV", MAdirectories = GEdirectories)
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('EpiMix_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: EpiMix
─ PackageVersion: 0.99.5
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpIm7CH6/filee9e2acbfe1a/EpiMix
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpIm7CH6/filee9e26cc3ac42
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
* Checking for deprecated package usage...
[230s/318s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
EpiMix 66.284 3.102 83.269
EpiMix_PlotGene 46.594 2.389 76.705
EpiMix_PlotProbe 26.462 0.642 46.030
GEO_Preprocess_DNAMethylation 11.949 0.211 13.899
TCGA_Preprocess_DNAmethylation 3.472 2.193 10.176
TCGA_Download_DNAmethylation 3.450 2.158 10.379
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
* 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 ...* 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 4.1.0 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:
Preprocessing
Search 'biocViews' at https://contributions.bioconductor.org
* 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 for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of EpiMix...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2558/5e1eab0e8be04988864ed3b839f1fbc2b836823a/EpiMix.Rcheck/00check.log’
for details.
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/overview.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 24
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 27
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
TCGA_GetData.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.1% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1565 lines (15%) are > 80
characters long.
* NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 2925 lines
(29%) are not.
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...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 19 NOTES
See the EpiMix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir EpiMix_0.99.5.tar.gz'
>>>>>>>
* installing *source* package ‘EpiMix’ ...
** using staged installation
** R
** 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 (EpiMix)