nebbiolo2 Summary
[top]
| Package: ceRNAR |
| Version: 0.99.10 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ceRNAR |
| BuildTime: 8 minutes 47.78 seconds |
| CheckCommand: BiocCheckGitClone('ceRNAR') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2847/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.install-out.txt ceRNAR_0.99.10.tar.gz && BiocCheck('ceRNAR_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 5.21 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2218.47 KiB |
| BuildID:: ceRNAR_20230730125518 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ceRNAR. 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: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘ceRNAR/DESCRIPTION’ ... OK
* preparing ‘ceRNAR’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘ceRNAR_0.99.10.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('ceRNAR')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ceRNAR
─ PackageVersion: 0.99.10
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
ceRNAR.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/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.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 ‘ceRNAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ceRNAR’ version ‘0.99.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'ggpubr', 'randomForest', 'zoo'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.Rcheck/00check.log’
for details.
===============================
BiocCheck('ceRNAR_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ceRNAR
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/Rtmpo8X0uU/file2819dd4b178afa/ceRNAR
─ installDir: /tmp/Rtmpo8X0uU/file2819dd53606ff2
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.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...
* NOTE: Consider adding these automatically suggested biocViews:
Network, Clustering
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
* WARNING: Import Biobase, biomaRt in NAMESPACE as well as
DESCRIPTION.
* WARNING: Import zoo, ggpubr, randomForest in DESCRIPTION as well
as NAMESPACE.
* 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 ceRNAR...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 26 functions greater than 50 lines.
* Checking man page documentation...
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
* 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; 453 lines (12%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1328 lines
(35%) 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 | 2 WARNINGS | 13 NOTES
See the ceRNAR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: ceRNAR |
| Version: 0.99.10 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ceRNAR |
| BuildTime: 5 minutes 42.36 seconds |
| CheckCommand: BiocCheckGitClone('ceRNAR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2847/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.install-out.txt ceRNAR_0.99.10.tar.gz && BiocCheck('ceRNAR_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 5.30 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ceRNAR_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 47.55 seconds |
| PackageFileSize: 2248.17 KiB |
| BuildID:: ceRNAR_20230730125518 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ceRNAR. 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: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘ceRNAR/DESCRIPTION’ ... OK
* preparing ‘ceRNAR’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘ceRNAR_0.99.10.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('ceRNAR')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ceRNAR
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
ceRNAR.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/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.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 ‘ceRNAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ceRNAR’ version ‘0.99.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'ggpubr', 'randomForest', 'zoo'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.Rcheck/00check.log’
for details.
===============================
BiocCheck('ceRNAR_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ceRNAR
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpmvAOWs/fileef6e68de8864/ceRNAR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpmvAOWs/fileef6e75c86386
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2847/37cbe6b7793cb3ad151e463ed52317c8cdcda3d3/ceRNAR.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...
* NOTE: Consider adding these automatically suggested biocViews:
Network, Clustering
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
* WARNING: Import Biobase, biomaRt in NAMESPACE as well as
DESCRIPTION.
* WARNING: Import zoo, ggpubr, randomForest in DESCRIPTION as well
as NAMESPACE.
* 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 ceRNAR...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 26 functions greater than 50 lines.
* Checking man page documentation...
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
* 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; 453 lines (12%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1328 lines
(35%) 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 | 2 WARNINGS | 13 NOTES
See the ceRNAR.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 ceRNAR_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘ceRNAR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘ceRNAR’
** testing if installed package keeps a record of temporary installation path
* DONE (ceRNAR)