nebbiolo1 Summary
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| Package: SimBu |
| Version: 0.99.6 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SimBu |
| BuildTime: 3 minutes 27.93 seconds |
| CheckCommand: BiocCheckGitClone('SimBu') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings SimBu_0.99.6.tar.gz && BiocCheck('SimBu_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 18.37 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 382.10 KiB |
| BuildID:: SimBu_20220525123844 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SimBu. 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 ‘SimBu/DESCRIPTION’ ... OK
* preparing ‘SimBu’:
* 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 ‘SimBu_0.99.6.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('SimBu')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: SimBu
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu
─ 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/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘0.99.6’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘SimBu’ can be installed ... [3s/3s] NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.Rcheck/00install.out’ for details.
* 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 ... [3s/3s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'dataset.Rd':
\examples lines wider than 100 characters:
ds <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset")
Rd file 'dataset_h5ad.Rd':
\examples lines wider than 100 characters:
cell_id_col = 'id', # this will use the 'id' column of the metadata as cell identifiers
cell_type_col = 'group', # this will use the 'group' column of the metadata as cell type inf ... [TRUNCATED]
cells_in_obs = TRUE) # in case your cell information is stored in the var layer, switch ... [TRUNCATED]
Rd file 'dataset_merge.Rd':
\examples lines wider than 100 characters:
ds1 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset1")
ds2 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset2")
Rd file 'dataset_sfaira.Rd':
\examples lines wider than 100 characters:
ds <- SimBu::dataset_sfaira(sfaira_id = 'homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x',
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 line endings in shell scripts ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [82s/70s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sfaira_overview 34.135 0.469 34.616
dataset_h5ad 4.451 9.989 2.993
simulate_bulk 11.424 1.012 12.435
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [59s/43s]
[59s/44s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.Rcheck/00check.log’
for details.
===============================
BiocCheck('SimBu_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: SimBu
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/Rtmp6TlMvL/file3d76125ff5dd96/SimBu
─ installDir: /tmp/Rtmp6TlMvL/file3d761262b449dd
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* 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...
* 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...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict 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 SimBu...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* 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
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 6
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.8% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* 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; 583 lines (15%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1179 lines
(31%) 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 | 1 WARNINGS | 13 NOTES
See the SimBu.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: SimBu |
| Version: 0.99.6 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SimBu |
| BuildTime: 9 minutes 42.75 seconds |
| CheckCommand: BiocCheckGitClone('SimBu') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SimBu_0.99.6.tar.gz && BiocCheck('SimBu_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 26.23 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh SimBu_0.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 10.88 seconds |
| PackageFileSize: 372.88 KiB |
| BuildID:: SimBu_20220525123844 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SimBu. 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: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘SimBu/DESCRIPTION’ ... OK
* preparing ‘SimBu’:
* 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 ‘SimBu_0.99.6.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('SimBu')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: SimBu
─ PackageVersion: 0.99.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu
─ 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/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘0.99.6’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘SimBu’ can be installed ... [10s/10s] NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.Rcheck/00install.out’ for details.
* 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 ... [9s/9s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'dataset.Rd':
\examples lines wider than 100 characters:
ds <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset")
Rd file 'dataset_h5ad.Rd':
\examples lines wider than 100 characters:
cell_id_col = 'id', # this will use the 'id' column of the metadata as cell identifiers
cell_type_col = 'group', # this will use the 'group' column of the metadata as cell type inf ... [TRUNCATED]
cells_in_obs = TRUE) # in case your cell information is stored in the var layer, switch ... [TRUNCATED]
Rd file 'dataset_merge.Rd':
\examples lines wider than 100 characters:
ds1 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset1")
ds2 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset2")
Rd file 'dataset_sfaira.Rd':
\examples lines wider than 100 characters:
ds <- SimBu::dataset_sfaira(sfaira_id = 'homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x',
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 line endings in shell scripts ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [195s/235s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sfaira_overview 102.398 1.034 129.165
simulate_bulk 26.241 1.639 27.936
dataset_h5ad 9.857 1.629 11.652
dataset 9.417 0.313 9.819
setup_sfaira 6.464 0.943 12.222
dataset_seurat 6.783 0.365 7.202
merge_simulations 5.955 0.096 6.088
plot_simulation 3.688 0.066 7.637
save_simulation 3.094 0.060 6.294
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [134s/135s]
[135s/135s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.Rcheck/00check.log’
for details.
===============================
BiocCheck('SimBu_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: SimBu
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpQhlUjl/filed4894caab2a3/SimBu
─ installDir: /tmp/RtmpQhlUjl/filed4896782c077
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2627/809ca04719449f434746c487e29b0ccf0e35779c/SimBu.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* 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...
* 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...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict 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 SimBu...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* 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
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 6
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.8% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* 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; 583 lines (15%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1179 lines
(31%) 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 | 1 WARNINGS | 13 NOTES
See the SimBu.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 SimBu_0.99.6.tar.gz'
>>>>>>>
* installing *source* package ‘SimBu’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (SimBu)