lconway Summary
[top]
| Package: staRgate |
| Version: 0.99.1 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data staRgate |
| BuildTime: 0 minutes 45.45 seconds |
| CheckCommand: BiocCheckGitClone('staRgate') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3485/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.install-out.txt staRgate_0.99.1.tar.gz && BiocCheck('staRgate_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 36.29 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh staRgate_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 2.53 seconds |
| PackageFileSize: 4819.76 KiB |
| BuildID:: staRgate_20240723132129 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: staRgate. 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. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘staRgate/DESCRIPTION’ ... OK
* preparing ‘staRgate’:
* 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
* building ‘staRgate_0.99.1.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('staRgate')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate
─ BiocVersion: 3.20
─ Package: staRgate
─ PackageVersion: 0.99.1
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘staRgate/DESCRIPTION’ ... OK
* this is package ‘staRgate’ version ‘0.99.1’
* 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 serialization versions ... OK
* checking whether package ‘staRgate’ can be installed ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [2s/3s] NOTE
getDensityDerivs: no visible binding for global variable ‘y’
getDensityDerivs: no visible binding for global variable ‘x_avg’
getDensityDerivs: no visible binding for global variable
‘original_row_num’
getDensityDerivs: no visible binding for global variable ‘y_avg’
getDensityDerivs: no visible binding for global variable ‘first_deriv’
getDensityDerivs: no visible binding for global variable ‘second_deriv’
getDensityDerivs: no visible binding for global variable ‘third_deriv’
getDensityDerivs: no visible binding for global variable
‘first_deriv_sign’
getDensityDerivs: no visible binding for global variable
‘second_deriv_sign’
getDensityDerivs: no visible binding for global variable
‘third_deriv_sign’
getDensityDerivs: no visible binding for global variable ‘fourth_deriv’
getDensityDerivs : <anonymous>: no visible binding for global variable
‘plateau_pre’
getDensityDerivs : <anonymous>: no visible binding for global variable
‘second_deriv_sign’
getDensityGates : <anonymous>: no visible binding for global variable
‘MARKER’
getDensityMats: no visible binding for global variable ‘data’
getDensityMats: no visible binding for global variable ‘dens_obj’
getDensityMats: no visible binding for global variable ‘dens_peaks’
getDensityMats : <anonymous>: no visible binding for global variable
‘peak’
getDensityMats : <anonymous>: no visible binding for global variable
‘x_avg’
getDensityMats: no visible binding for global variable ‘peak_loc’
getDensityMats: no visible binding for global variable ‘flag_pos_peak’
getDensityMats: no visible binding for global variable
‘dens_peaks_flip’
getDensityMats : <anonymous>: no visible binding for global variable
‘cutoff’
getDensityMats : <anonymous>: no visible binding for global variable
‘original_row_num’
getDensityPeakCutoff: no visible binding for global variable
‘local_peak’
getDensityPeakCutoff: no visible binding for global variable ‘y_avg’
getDensityPeakCutoff : <anonymous>: no visible binding for global
variable ‘y_avg’
getDensityPeakCutoff: no visible binding for global variable ‘ratio’
getDensityPeakCutoff: no visible binding for global variable
‘original_row_num’
getDensityPeakCutoff: no visible binding for global variable ‘peak’
getDensityPeakCutoff: no visible binding for global variable
‘plateau_pre_2’
getGatedDat: no visible binding for global variable ‘intensity_dat’
getGatedDat: no visible binding for global variable ‘data’
getGatedDat: no visible binding for global variable ‘gated_data’
getPerc: no visible binding for global variable ‘denom_filters’
Undefined global functions or variables:
MARKER cutoff data denom_filters dens_obj dens_peaks dens_peaks_flip
first_deriv first_deriv_sign flag_pos_peak fourth_deriv gated_data
intensity_dat local_peak original_row_num peak peak_loc plateau_pre
plateau_pre_2 ratio second_deriv second_deriv_sign third_deriv
third_deriv_sign x_avg y y_avg
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[4s/4s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.Rcheck/00check.log’
for details.
===============================
BiocCheck('staRgate_0.99.1.tar.gz')
===============================
* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpckS7Nx/file88bf767cc0ee/staRgate
─ BiocVersion: 3.20
─ Package: staRgate
─ PackageVersion: 0.99.1
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpckS7Nx/file88bf767cc0ee/staRgate
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpckS7Nx/file88bf785e8607
─ isTarBall: TRUE
─ platform: unix
* 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...
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of staRgate...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/vignette_run_pipeline.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 242 lines (10%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 67 lines (3%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 947 lines
(39%) are not.
See https://contributions.bioconductor.org/r-code.html
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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 8 NOTES
See the staRgate.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir staRgate_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘staRgate’ ...
** 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 (staRgate)
nebbiolo2 Summary
[top]
| Package: staRgate |
| Version: 0.99.1 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data staRgate |
| BuildTime: 1 minutes 0.52 seconds |
| CheckCommand: BiocCheckGitClone('staRgate') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3485/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.install-out.txt staRgate_0.99.1.tar.gz && BiocCheck('staRgate_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 32.87 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4438.92 KiB |
| BuildID:: staRgate_20240723132129 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: staRgate. 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. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘staRgate/DESCRIPTION’ ... OK
* preparing ‘staRgate’:
* 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
* building ‘staRgate_0.99.1.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('staRgate')
===============================
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate
─ BiocVersion: 3.20
─ Package: staRgate
─ PackageVersion: 0.99.1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘staRgate/DESCRIPTION’ ... OK
* this is package ‘staRgate’ version ‘0.99.1’
* 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 serialization versions ... OK
* checking whether package ‘staRgate’ can be installed ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] NOTE
getDensityDerivs: no visible binding for global variable ‘y’
getDensityDerivs: no visible binding for global variable ‘x_avg’
getDensityDerivs: no visible binding for global variable
‘original_row_num’
getDensityDerivs: no visible binding for global variable ‘y_avg’
getDensityDerivs: no visible binding for global variable ‘first_deriv’
getDensityDerivs: no visible binding for global variable ‘second_deriv’
getDensityDerivs: no visible binding for global variable ‘third_deriv’
getDensityDerivs: no visible binding for global variable
‘first_deriv_sign’
getDensityDerivs: no visible binding for global variable
‘second_deriv_sign’
getDensityDerivs: no visible binding for global variable
‘third_deriv_sign’
getDensityDerivs: no visible binding for global variable ‘fourth_deriv’
getDensityDerivs : <anonymous>: no visible binding for global variable
‘plateau_pre’
getDensityDerivs : <anonymous>: no visible binding for global variable
‘second_deriv_sign’
getDensityGates : <anonymous>: no visible binding for global variable
‘MARKER’
getDensityMats: no visible binding for global variable ‘data’
getDensityMats: no visible binding for global variable ‘dens_obj’
getDensityMats: no visible binding for global variable ‘dens_peaks’
getDensityMats : <anonymous>: no visible binding for global variable
‘peak’
getDensityMats : <anonymous>: no visible binding for global variable
‘x_avg’
getDensityMats: no visible binding for global variable ‘peak_loc’
getDensityMats: no visible binding for global variable ‘flag_pos_peak’
getDensityMats: no visible binding for global variable
‘dens_peaks_flip’
getDensityMats : <anonymous>: no visible binding for global variable
‘cutoff’
getDensityMats : <anonymous>: no visible binding for global variable
‘original_row_num’
getDensityPeakCutoff: no visible binding for global variable
‘local_peak’
getDensityPeakCutoff: no visible binding for global variable ‘y_avg’
getDensityPeakCutoff : <anonymous>: no visible binding for global
variable ‘y_avg’
getDensityPeakCutoff: no visible binding for global variable ‘ratio’
getDensityPeakCutoff: no visible binding for global variable
‘original_row_num’
getDensityPeakCutoff: no visible binding for global variable ‘peak’
getDensityPeakCutoff: no visible binding for global variable
‘plateau_pre_2’
getGatedDat: no visible binding for global variable ‘intensity_dat’
getGatedDat: no visible binding for global variable ‘data’
getGatedDat: no visible binding for global variable ‘gated_data’
getPerc: no visible binding for global variable ‘denom_filters’
Undefined global functions or variables:
MARKER cutoff data denom_filters dens_obj dens_peaks dens_peaks_flip
first_deriv first_deriv_sign flag_pos_peak fourth_deriv gated_data
intensity_dat local_peak original_row_num peak peak_loc plateau_pre
plateau_pre_2 ratio second_deriv second_deriv_sign third_deriv
third_deriv_sign x_avg y y_avg
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/6s]
[6s/6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.Rcheck/00check.log’
for details.
===============================
BiocCheck('staRgate_0.99.1.tar.gz')
===============================
* Installing package...
─ sourceDir: /tmp/RtmpPXAEyF/file31a78a66d1ff13/staRgate
─ BiocVersion: 3.20
─ Package: staRgate
─ PackageVersion: 0.99.1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3485/1dd51d12157d6772b103db28a8cb29bbfbbb97a7/staRgate.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /tmp/RtmpPXAEyF/file31a78a66d1ff13/staRgate
─ installDir: /tmp/RtmpPXAEyF/file31a78afa7fdf0
─ isTarBall: TRUE
─ platform: unix
* 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...
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of staRgate...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/vignette_run_pipeline.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 242 lines (10%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 67 lines (3%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 947 lines
(39%) are not.
See https://contributions.bioconductor.org/r-code.html
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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 8 NOTES
See the staRgate.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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