merida1 Summary
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| Package: DELocal |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DELocal |
| BuildTime: 0 minutes 28.39 seconds |
| CheckCommand: BiocCheckGitClone('DELocal') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2916/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.install-out.txt DELocal_0.99.1.tar.gz && BiocCheck('DELocal_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 39.82 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DELocal_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 5.09 seconds |
| PackageFileSize: 1644.19 KiB |
| BuildID:: DELocal_20230222175254 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DELocal. 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. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘DELocal/DESCRIPTION’ ... OK
* preparing ‘DELocal’:
* 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 ‘DELocal_0.99.1.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('DELocal')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: DELocal
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
DELocal.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...
* NOTE: CITATION file might be not correctly formatted
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.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 ‘DELocal/DESCRIPTION’ ... OK
* this is package ‘DELocal’ version ‘0.99.1’
* 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 serialization versions ... OK
* checking whether package ‘DELocal’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 5.7Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [6s/6s] NOTE
LocalizedLinearModel: no visible binding for global variable
‘chromosome_name’
LocalizedLinearModel: no visible binding for global variable
‘start_position’
getNeighbours: no visible binding for global variable ‘chromosome_name’
getNeighbours: no visible binding for global variable ‘start_position’
optimize_Local: no visible binding for global variable
‘ensembl_gene_id’
plotNeighbourhood: no visible binding for global variable
‘start_position’
plotNeighbourhood: no visible binding for global variable ‘value’
plotNeighbourhood: no visible binding for global variable
‘ensembl_gene_id’
plotNeighbourhood: no visible binding for global variable ‘variable’
plot_LOCAL_lm: no visible binding for global variable ‘chromosome_name’
plot_LOCAL_lm: no visible binding for global variable ‘start_position’
plot_LOCAL_lm: no visible global function definition for ‘lm’
rnaSeq_rank : makeRank: no visible global function definition for ‘n’
rnaSeq_rank : makeRank: no visible binding for global variable
‘tooth_genes’
rnaSeq_rank : makeRank: no visible binding for global variable
‘ensembl_gene_id’
rnaSeq_rank : makeRank: no visible binding for global variable
‘sequence_rank’
roc_from_topGenes: no visible binding for global variable
‘FCros_e13wt_vs_e14wt’
Undefined global functions or variables:
FCros_e13wt_vs_e14wt chromosome_name ensembl_gene_id lm n
sequence_rank start_position tooth_genes value variable
Consider adding
importFrom("stats", "lm")
to your NAMESPACE file.
* 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 ... NONE
* 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 ... [4s/4s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.Rcheck/00check.log’
for details.
===============================
BiocCheck('DELocal_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: DELocal
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpAp3hVc/file11edf291f508e/DELocal
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpAp3hVc/file11edfad7bf0a
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.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...
* 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 DELocal...
* 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 in cond & parsedf$token[which(cond) - 1] != shQuote(lookback) :
longer object length is not a multiple of shorter object length
* 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 20 functions greater than 50 lines.
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* 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; 151 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 305 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...
* 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
3 ERRORS | 2 WARNINGS | 8 NOTES
See the DELocal.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DELocal_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘DELocal’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (DELocal)
nebbiolo1 Summary
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| Package: DELocal |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DELocal |
| BuildTime: 0 minutes 21.96 seconds |
| CheckCommand: BiocCheckGitClone('DELocal') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2916/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.install-out.txt DELocal_0.99.1.tar.gz && BiocCheck('DELocal_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 31.80 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1644.32 KiB |
| BuildID:: DELocal_20230222175254 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DELocal. 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. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘DELocal/DESCRIPTION’ ... OK
* preparing ‘DELocal’:
* 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 ‘DELocal_0.99.1.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('DELocal')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: DELocal
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
DELocal.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...
* NOTE: CITATION file might be not correctly formatted
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.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 ‘DELocal/DESCRIPTION’ ... OK
* this is package ‘DELocal’ version ‘0.99.1’
* 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 serialization versions ... OK
* checking whether package ‘DELocal’ 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 ... NOTE
Malformed Title field: should not end in a period.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] NOTE
LocalizedLinearModel: no visible binding for global variable
‘chromosome_name’
LocalizedLinearModel: no visible binding for global variable
‘start_position’
getNeighbours: no visible binding for global variable ‘chromosome_name’
getNeighbours: no visible binding for global variable ‘start_position’
optimize_Local: no visible binding for global variable
‘ensembl_gene_id’
plotNeighbourhood: no visible binding for global variable
‘start_position’
plotNeighbourhood: no visible binding for global variable ‘value’
plotNeighbourhood: no visible binding for global variable
‘ensembl_gene_id’
plotNeighbourhood: no visible binding for global variable ‘variable’
plot_LOCAL_lm: no visible binding for global variable ‘chromosome_name’
plot_LOCAL_lm: no visible binding for global variable ‘start_position’
plot_LOCAL_lm: no visible global function definition for ‘lm’
rnaSeq_rank : makeRank: no visible global function definition for ‘n’
rnaSeq_rank : makeRank: no visible binding for global variable
‘tooth_genes’
rnaSeq_rank : makeRank: no visible binding for global variable
‘ensembl_gene_id’
rnaSeq_rank : makeRank: no visible binding for global variable
‘sequence_rank’
roc_from_topGenes: no visible binding for global variable
‘FCros_e13wt_vs_e14wt’
Undefined global functions or variables:
FCros_e13wt_vs_e14wt chromosome_name ensembl_gene_id lm n
sequence_rank start_position tooth_genes value variable
Consider adding
importFrom("stats", "lm")
to your NAMESPACE file.
* 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 ... NONE
* 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 ... [2s/2s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.Rcheck/00check.log’
for details.
===============================
BiocCheck('DELocal_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: DELocal
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmpqkb75Y/file310b8363b6fd60/DELocal
─ installDir: /tmp/Rtmpqkb75Y/file310b835723420c
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2916/DELocal_20230222175254/DELocal.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...
* 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 DELocal...
* 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 in cond & parsedf$token[which(cond) - 1] != shQuote(lookback) :
longer object length is not a multiple of shorter object length
* 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 20 functions greater than 50 lines.
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* 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; 151 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 305 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...
* 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
3 ERRORS | 2 WARNINGS | 8 NOTES
See the DELocal.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]