nebbiolo1 Summary
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| Package: scMultiome |
| Version: 0.99.11 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scMultiome |
| BuildTime: 1 minutes 29.85 seconds |
| CheckCommand: BiocCheckGitClone('scMultiome') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2901/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.install-out.txt scMultiome_0.99.11.tar.gz && BiocCheck('scMultiome_0.99.11.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 37.24 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 342.87 KiB |
| BuildID:: scMultiome_20230320213150 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scMultiome. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘scMultiome/DESCRIPTION’ ... OK
* preparing ‘scMultiome’:
* 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 ‘scMultiome_0.99.11.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('scMultiome')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: scMultiome
─ PackageVersion: 0.99.11
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome
─ 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...
─ 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/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* 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 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMultiome/DESCRIPTION’ ... OK
* this is package ‘scMultiome’ version ‘0.99.11’
* 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 ‘scMultiome’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [17s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/19s] OK
* checking loading without being on the library search path ... [0s/0s] WARNING
Error: package ‘AnnotationHub’ required by ‘scMultiome’ could not be found
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... [53s/54s] OK
* 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 ... [0s/0s] ERROR
Running examples in ‘scMultiome-Ex.R’ failed
The error occurred in:
R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "scMultiome"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "scMultiome-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+ options(OutDec = '.')
+ format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
>
> ### * </HEADER>
> library('scMultiome')
Error: package ‘AnnotationHub’ required by ‘scMultiome’ could not be found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [0s/0s]
[1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
Error in library(testthat) : there is no package called 'testthat'
Execution halted
* 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 ... [5s/6s] OK
* DONE
Status: 2 ERRORs, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.Rcheck/00check.log’
for details.
===============================
BiocCheck('scMultiome_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: scMultiome
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/RtmpOsmtWy/file720bf3242b96b/scMultiome
─ installDir: /tmp/RtmpOsmtWy/file720bf9e35015
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Evaluate more vignette chunks.
11 code chunks / 19 total = 57% percent unevaluated
0 non-exec code chunks (e.g., '``` r')
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scMultiome...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 38% of man pages use at least one of these tags.
* 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; 350 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 123 lines
(3%) 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 | 6 NOTES
See the scMultiome.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: scMultiome |
| Version: 0.99.11 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scMultiome |
| BuildTime: 1 minutes 49.32 seconds |
| CheckCommand: BiocCheckGitClone('scMultiome') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2901/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.install-out.txt scMultiome_0.99.11.tar.gz && BiocCheck('scMultiome_0.99.11.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 31.60 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh scMultiome_0.99.11.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 9.59 seconds |
| PackageFileSize: 342.85 KiB |
| BuildID:: scMultiome_20230320213150 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scMultiome. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. 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 ‘scMultiome/DESCRIPTION’ ... OK
* preparing ‘scMultiome’:
* 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 ‘scMultiome_0.99.11.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('scMultiome')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: scMultiome
─ PackageVersion: 0.99.11
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome
─ 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...
─ 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/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* 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 ‘scMultiome/DESCRIPTION’ ... OK
* this is package ‘scMultiome’ version ‘0.99.11’
* 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 ‘scMultiome’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [19s/21s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/22s] OK
* checking whether the package can be unloaded cleanly ... [19s/21s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/21s] OK
* checking loading without being on the library search path ... [20s/22s] 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 ... [64s/71s] OK
* 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 ... [61s/72s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fileOperations 18.304 0.356 20.162
dummies 6.761 0.169 7.375
colonHealthy 1.430 0.122 7.827
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [87s/95s]
[88s/96s] 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 ... [10s/11s] OK
* DONE
Status: OK
===============================
BiocCheck('scMultiome_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: scMultiome
─ PackageVersion: 0.99.11
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpoJJ450/file653528907c7/scMultiome
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpoJJ450/file65355f72c793
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2901/4bff4390a4792ac2df561c72f8b38c9b346981de/scMultiome.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Evaluate more vignette chunks.
11 code chunks / 19 total = 57% percent unevaluated
0 non-exec code chunks (e.g., '``` r')
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scMultiome...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 38% of man pages use at least one of these tags.
* 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; 350 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 123 lines
(3%) 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 | 6 NOTES
See the scMultiome.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 scMultiome_0.99.11.tar.gz'
>>>>>>>
* installing *source* package ‘scMultiome’ ...
** 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 (scMultiome)