nebbiolo1 Summary
[top]
| Package: scFeatures |
| Version: 0.99.17 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scFeatures |
| BuildTime: 5 minutes 59.88 seconds |
| CheckCommand: BiocCheckGitClone('scFeatures') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2815/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.install-out.txt scFeatures_0.99.17.tar.gz && BiocCheck('scFeatures_0.99.17.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 12.75 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4864.26 KiB |
| BuildID:: scFeatures_20230119073709 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scFeatures. 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. WARNING: check time exceeded 10 min. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* preparing ‘scFeatures’:
* 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 ‘scFeatures_0.99.17.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('scFeatures')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scFeatures
─ PackageVersion: 0.99.17
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ 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/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* this is package ‘scFeatures’ version ‘0.99.17’
* 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 ‘scFeatures’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [17s/17s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the package can be unloaded cleanly ... [16s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/17s] OK
* checking loading without being on the library search path ... [17s/17s] 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 ... [54s/54s] NOTE
helper_CCI: no visible binding for global variable 'LRdb'
helper_CCI: no visible global function definition for 'capture.output'
run_pathway_gsva: no visible global function definition for
'capture.output'
Undefined global functions or variables:
LRdb capture.output
Consider adding
importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘scFeatures/R/helper_CCI.R’:
data(LRdb, package = "SingleCellSignalR")
See section ‘Good practice’ in ‘?data’.
* 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 ... [456s/274s] WARNING
Found the following significant warnings:
Warning: working directory was changed to '/tmp/RtmpfWzKjs', resetting
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_gene_cor_celltype 205.464 20.089 64.002
run_Morans_I 62.720 0.762 63.488
run_gene_prop_celltype 17.744 3.703 15.163
run_gene_mean_celltype 19.485 1.027 14.793
run_pathway_prop 18.188 0.452 18.641
run_pathway_mean 12.456 0.434 12.891
run_pathway_gsva 11.747 0.577 12.325
remove_mito 1.898 6.428 0.656
run_gene_cor 5.443 0.221 4.670
* 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 ... [3s/3s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('scFeatures_0.99.17.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scFeatures
─ PackageVersion: 0.99.17
─ sourceDir: /tmp/RtmpV5XbyO/file1557ef47174aed/scFeatures
─ installDir: /tmp/RtmpV5XbyO/file1557ef3fefcb88
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 4.2.0 to 4.3.0.
* 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...
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scFeatures...
* Checking coding practice...
* 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
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/scFeatures_detail.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 99 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 4% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 314 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 513 lines
(8%) 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 name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 15 NOTES
See the scFeatures.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: scFeatures |
| Version: 0.99.17 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scFeatures |
| BuildTime: 11 minutes 45.83 seconds |
| CheckCommand: BiocCheckGitClone('scFeatures') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2815/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.install-out.txt scFeatures_0.99.17.tar.gz && BiocCheck('scFeatures_0.99.17.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.96 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh scFeatures_0.99.17.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 2 minutes 32.61 seconds |
| PackageFileSize: 4863.29 KiB |
| BuildID:: scFeatures_20230119073709 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scFeatures. 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. WARNING: check time exceeded 10 min. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* preparing ‘scFeatures’:
* 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 ‘scFeatures_0.99.17.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('scFeatures')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scFeatures
─ PackageVersion: 0.99.17
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ 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/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* this is package ‘scFeatures’ version ‘0.99.17’
* 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 ‘scFeatures’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [39s/43s] OK
* checking whether the package can be loaded with stated dependencies ... [37s/42s] OK
* checking whether the package can be unloaded cleanly ... [38s/42s] OK
* checking whether the namespace can be loaded with stated dependencies ... [38s/42s] OK
* checking whether the namespace can be unloaded cleanly ... [39s/45s] OK
* checking loading without being on the library search path ... [39s/45s] 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 ... [129s/145s] NOTE
helper_CCI: no visible binding for global variable 'LRdb'
helper_CCI: no visible global function definition for 'capture.output'
run_pathway_gsva: no visible global function definition for
'capture.output'
Undefined global functions or variables:
LRdb capture.output
Consider adding
importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘scFeatures/R/helper_CCI.R’:
data(LRdb, package = "SingleCellSignalR")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('scFeatures_0.99.17.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scFeatures
─ PackageVersion: 0.99.17
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpSjKEZG/file147152cb5605/scFeatures
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpSjKEZG/file147145fb1989
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2815/051d25161b932b9ca771c5f374560aae73a5ebaa/scFeatures.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 4.2.0 to 4.3.0.
* 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...
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scFeatures...
* Checking coding practice...
* 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
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/scFeatures_detail.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 99 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 4% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 314 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 513 lines
(8%) 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 name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 15 NOTES
See the scFeatures.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 scFeatures_0.99.17.tar.gz'
>>>>>>>
* installing *source* package ‘scFeatures’ ...
** 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 (scFeatures)