nebbiolo2 Summary
[top]
| Package: multiWGCNA |
| Version: 0.99.0 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data multiWGCNA |
| BuildTime: 3 minutes 1.48 seconds |
| CheckCommand: BiocCheckGitClone('multiWGCNA') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3063/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.install-out.txt multiWGCNA_0.99.0.tar.gz && BiocCheck('multiWGCNA_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 4.77 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 709.39 KiB |
| BuildID:: multiWGCNA_20230623153737 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: multiWGCNA. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 3. Build Package status: 0. Checking Package status: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* preparing ‘multiWGCNA’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘multiWGCNA_0.99.0.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('multiWGCNA')
===============================
─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
multiWGCNA.Rproj
* 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 ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiWGCNA’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.github
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 whether package ‘multiWGCNA’ can be installed ... ERROR
Installation failed.
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.Rcheck/00check.log’
for details.
===============================
BiocCheck('multiWGCNA_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmp5iqipX/file193abf6c790b99/multiWGCNA
─ installDir: /tmp/Rtmp5iqipX/file193abf34ef609c
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.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...
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...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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...
* WARNING: Import grDevices, graphics, stats, utils in DESCRIPTION
as well as NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of multiWGCNA...
* 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...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 7 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* 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...
* 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; 301 lines (9%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1038 lines (32%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 235 lines
(7%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 5 WARNINGS | 11 NOTES
See the multiWGCNA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: multiWGCNA |
| Version: 0.99.0 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data multiWGCNA |
| BuildTime: 2 minutes 24.58 seconds |
| CheckCommand: BiocCheckGitClone('multiWGCNA') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3063/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.install-out.txt multiWGCNA_0.99.0.tar.gz && BiocCheck('multiWGCNA_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 11.25 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh multiWGCNA_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 21.76 seconds |
| PackageFileSize: 773.31 KiB |
| BuildID:: multiWGCNA_20230623153737 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: multiWGCNA. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 3. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* preparing ‘multiWGCNA’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘multiWGCNA_0.99.0.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('multiWGCNA')
===============================
─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
multiWGCNA.Rproj
* 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 ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiWGCNA’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.github
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 whether package ‘multiWGCNA’ can be installed ... ERROR
Installation failed.
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.Rcheck/00check.log’
for details.
===============================
BiocCheck('multiWGCNA_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpIPp4Nj/filee8f32363368/multiWGCNA
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpIPp4Nj/filee8fc36c512
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3063/multiWGCNA_20230623153737/multiWGCNA.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...
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...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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...
* WARNING: Import grDevices, graphics, stats, utils in DESCRIPTION
as well as NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of multiWGCNA...
* 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...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 7 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* 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...
* 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; 301 lines (9%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1038 lines (32%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 235 lines
(7%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 5 WARNINGS | 11 NOTES
See the multiWGCNA.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 multiWGCNA_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘multiWGCNA’ ...
** 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 (multiWGCNA)