merida1 Summary
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| Package: extraChIPs |
| Version: 0.99.0 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data extraChIPs |
| BuildTime: 2 minutes 22.70 seconds |
| CheckCommand: BiocCheckGitClone('extraChIPs') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch extraChIPs_0.99.0.tar.gz && BiocCheck('extraChIPs_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 29.92 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh extraChIPs_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 57.92 seconds |
| PackageFileSize: 2006.03 KiB |
| BuildID:: extraChIPs_20220405142611 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: extraChIPs. 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
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===============================
R CMD BUILD
===============================
* checking for file ‘extraChIPs/DESCRIPTION’ ... OK
* preparing ‘extraChIPs’:
* 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 ‘extraChIPs_0.99.0.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('extraChIPs')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2598/extraChIPs_20220405142611/extraChIPs.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘extraChIPs/DESCRIPTION’ ... OK
* this is package ‘extraChIPs’ version ‘0.99.0’
* 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 ‘extraChIPs’ can be installed ... [56s/56s] 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 ... [60s/60s] OK
* 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 ... [60s/60s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotHFGC 7.301 0.044 7.345
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [57s/64s]
[57s/64s] 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: OK
===============================
BiocCheck('extraChIPs_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2598/extraChIPs_20220405142611/extraChIPs_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpfyw6a3/file1df1df297b9/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 4.1.0 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:
ChipOnChip, Coverage
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...
* NOTE: License 'file LICENSE' unknown; licenses cannot restrict
use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/differential_binding.Rmd
vignettes/range_based_functions.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of extraChIPs...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/partitionRanges.R (line 55, column 46)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressWarnings() in R/importPeaks.R (line 109, column 20)
suppressWarnings() in R/importPeaks.R (line 122, column 20)
suppressWarnings() in R/mapByFeature.R (line 365, column 16)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 15 functions > 50 lines.
The longest 5 functions are:
.checkCoverage() (R/plotHFGC.R, line 741): 117 lines
.checkGenes() (R/plotHFGC.R, line 858): 96 lines
plotHFGC() (R/plotHFGC.R, line 282): 83 lines
.plotTriplePie() (R/plotPie.R, line 303): 62 lines
.plotDoublePie() (R/plotPie.R, line 234): 61 lines
* Checking man page documentation...
Registered S3 method overwritten by 'ggside':
method from
+.gg ggplot2
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
dualFilter-methods.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; 42 lines (1%) are > 80 characters
long.
First 6 lines:
R/data.R:24 #' @source \url{https://hgdownload.soe.ucsc.edu/goldenPath/...
R/data.R:25 #' @source \url{https://hgdownload.soe.ucsc.edu/goldenPath/...
man/as_tibble.Rd:17 \method{as_tibble}{GInteractions}(x, rangeAsChar = ...
man/dualFilter-methods.Rd:5 \alias{dualFilter,RangedSummarizedExperimen...
man/dualFilter-methods.Rd:11 \S4method{dualFilter}{RangedSummarizedExpe...
man/dualFilter-methods.Rd:62 In general, higher values of \code{q} will...
* NOTE: Consider multiples of 4 spaces for line indents, 1636
lines(20%) are not.
First 6 lines:
R/AllGenerics.R:5 "bestOverlap", function(x, y, ...) standardGeneric(...
R/AllGenerics.R:12 "chopMC", function(x, simplify = TRUE, ...) standa...
R/AllGenerics.R:19 "colToRanges", function(x, var, ...) standardGener...
R/AllGenerics.R:26 "distinctMC",
R/AllGenerics.R:27 function(x, cols, ...) standardGeneric("distinctMC")
R/AllGenerics.R:34 "dualFilter", function(x, bg, ref, ...) standardGe...
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 2
WARNING count: 0
NOTE count: 10
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.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir extraChIPs_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘extraChIPs’ ...
** 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 (extraChIPs)
nebbiolo1 Summary
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| Package: extraChIPs |
| Version: 0.99.0 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data extraChIPs |
| BuildTime: 1 minutes 46.86 seconds |
| CheckCommand: BiocCheckGitClone('extraChIPs') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings extraChIPs_0.99.0.tar.gz && BiocCheck('extraChIPs_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 53.01 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2020.65 KiB |
| BuildID:: extraChIPs_20220405142611 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: extraChIPs. 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 ‘extraChIPs/DESCRIPTION’ ... OK
* preparing ‘extraChIPs’:
* 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 ‘extraChIPs_0.99.0.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('extraChIPs')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2598/extraChIPs_20220405142611/extraChIPs.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘extraChIPs/DESCRIPTION’ ... OK
* this i* this is package ‘extraChIPs’ version ‘0.99.0’
* 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 ‘extraChIPs’ 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 ... [43s/43s] OK
* 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 ... [51s/51s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotHFGC 6.002 0.116 6.118
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [42s/45s]
[43s/45s] 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: OK
===============================
BiocCheck('extraChIPs_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2598/extraChIPs_20220405142611/extraChIPs_0.99.0.tar.gz" "/tmp/Rtmpyc1qKB/file12887b5aa36fa0/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 4.1.0 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:
ChipOnChip, Coverage
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...
* NOTE: License 'file LICENSE' unknown; licenses cannot restrict
use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/differential_binding.Rmd
vignettes/range_based_functions.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of extraChIPs...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/partitionRanges.R (line 55, column 46)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressWarnings() in R/importPeaks.R (line 109, column 20)
suppressWarnings() in R/importPeaks.R (line 122, column 20)
suppressWarnings() in R/mapByFeature.R (line 365, column 16)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 15 functions > 50 lines.
The longest 5 functions are:
.checkCoverage() (R/plotHFGC.R, line 741): 117 lines
.checkGenes() (R/plotHFGC.R, line 858): 96 lines
plotHFGC() (R/plotHFGC.R, line 282): 83 lines
.plotTriplePie() (R/plotPie.R, line 303): 62 lines
.plotDoublePie() (R/plotPie.R, line 234): 61 lines
* Checking man page documentation...
Registered S3 method overwritten by 'ggside':
method from
+.gg ggplot2
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
dualFilter-methods.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; 42 lines (1%) are > 80 characters
long.
First 6 lines:
R/data.R:24 #' @source \url{https://hgdownload.soe.ucsc.edu/goldenPath/...
R/data.R:25 #' @source \url{https://hgdownload.soe.ucsc.edu/goldenPath/...
man/as_tibble.Rd:17 \method{as_tibble}{GInteractions}(x, rangeAsChar = ...
man/dualFilter-methods.Rd:5 \alias{dualFilter,RangedSummarizedExperimen...
man/dualFilter-methods.Rd:11 \S4method{dualFilter}{RangedSummarizedExpe...
man/dualFilter-methods.Rd:62 In general, higher values of \code{q} will...
* NOTE: Consider multiples of 4 spaces for line indents, 1636
lines(20%) are not.
First 6 lines:
R/AllGenerics.R:5 "bestOverlap", function(x, y, ...) standardGeneric(...
R/AllGenerics.R:12 "chopMC", function(x, simplify = TRUE, ...) standa...
R/AllGenerics.R:19 "colToRanges", function(x, var, ...) standardGener...
R/AllGenerics.R:26 "distinctMC",
R/AllGenerics.R:27 function(x, cols, ...) standardGeneric("distinctMC")
R/AllGenerics.R:34 "dualFilter", function(x, bg, ref, ...) standardGe...
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 2
WARNING count: 0
NOTE count: 10
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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