lconway Summary
[top]
| Package: immunogenViewer |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data immunogenViewer |
| BuildTime: 0 minutes 22.95 seconds |
| CheckCommand: BiocCheckGitClone('immunogenViewer') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3446/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.install-out.txt immunogenViewer_0.99.3.tar.gz && BiocCheck('immunogenViewer_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 48.11 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh immunogenViewer_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 9.59 seconds |
| PackageFileSize: 657.87 KiB |
| BuildID:: immunogenViewer_20240722173054 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: immunogenViewer. 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. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file immunogenViewer/DESCRIPTION ... OK
* preparing immunogenViewer:
* 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 immunogenViewer_0.99.3.tar.gz
lconway CHECK output
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===============================
BiocCheckGitClone('immunogenViewer')
===============================
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer
BiocVersion: 3.20
Package: immunogenViewer
PackageVersion: 0.99.3
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file immunogenViewer/DESCRIPTION ... OK
* checking extension type ... Package
* this is package immunogenViewer version 0.99.3
* 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 immunogenViewer 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [10s/10s] NOTE
addImmunogensToPlot: no visible binding for global variable xmin
addImmunogensToPlot: no visible binding for global variable xmax
addImmunogensToPlot: no visible binding for global variable ymin
addImmunogensToPlot: no visible binding for global variable ymax
addImmunogensToPlot: no visible binding for global variable x
addImmunogensToPlot: no visible binding for global variable y
addImmunogensToPlot: no visible binding for global variable label
plotAccessibility: no visible binding for global variable
SolventAccessibility
plotSecondaryStructure: no visible binding for global variable
SecondaryStructure
plotSinglePositions: no visible binding for global variable Location
plotSinglePositions: no visible binding for global variable y
Undefined global functions or variables:
Location SecondaryStructure SolventAccessibility label x xmax xmin y
ymax ymin
* 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 ... [6s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [6s/19s]
[6s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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: 1 NOTE
See
/Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.Rcheck/00check.log
for details.
===============================
BiocCheck('immunogenViewer_0.99.3.tar.gz')
===============================
* Installing package...
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3zL4D0/file1a0841e8ff70/immunogenViewer
BiocVersion: 3.20
Package: immunogenViewer
PackageVersion: 0.99.3
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3zL4D0/file1a0841e8ff70/immunogenViewer
installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3zL4D0/file1a0827da33de
isTarBall: TRUE
platform: unix
* 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 4.0 to 4.4.0.
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of immunogenViewer...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 94 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 292 lines
(28%) 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 is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 1 WARNINGS | 8 NOTES
See the immunogenViewer.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 immunogenViewer_0.99.3.tar.gz'
>>>>>>>
* installing *source* package immunogenViewer ...
** 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 (immunogenViewer)
nebbiolo2 Summary
[top]
| Package: immunogenViewer |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data immunogenViewer |
| BuildTime: 0 minutes 29.75 seconds |
| CheckCommand: BiocCheckGitClone('immunogenViewer') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3446/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.install-out.txt immunogenViewer_0.99.3.tar.gz && BiocCheck('immunogenViewer_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 13.53 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 605.72 KiB |
| BuildID:: immunogenViewer_20240722173054 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: immunogenViewer. 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. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file immunogenViewer/DESCRIPTION ... OK
* preparing immunogenViewer:
* 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 immunogenViewer_0.99.3.tar.gz
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('immunogenViewer')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer
BiocVersion: 3.20
Package: immunogenViewer
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file immunogenViewer/DESCRIPTION ... OK
* checking extension type ... Package
* this is package immunogenViewer version 0.99.3
* 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 immunogenViewer 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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 ... [14s/14s] NOTE
addImmunogensToPlot: no visible binding for global variable xmin
addImmunogensToPlot: no visible binding for global variable xmax
addImmunogensToPlot: no visible binding for global variable ymin
addImmunogensToPlot: no visible binding for global variable ymax
addImmunogensToPlot: no visible binding for global variable x
addImmunogensToPlot: no visible binding for global variable y
addImmunogensToPlot: no visible binding for global variable label
plotAccessibility: no visible binding for global variable
SolventAccessibility
plotSecondaryStructure: no visible binding for global variable
SecondaryStructure
plotSinglePositions: no visible binding for global variable Location
plotSinglePositions: no visible binding for global variable y
Undefined global functions or variables:
Location SecondaryStructure SolventAccessibility label x xmax xmin y
ymax ymin
* 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 ... [9s/19s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [10s/22s]
[10s/22s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.Rcheck/00check.log
for details.
===============================
BiocCheck('immunogenViewer_0.99.3.tar.gz')
===============================
* Installing package...
sourceDir: /tmp/RtmpEyKP7F/file27d88149b509f3/immunogenViewer
BiocVersion: 3.20
Package: immunogenViewer
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3446/2d38335543845c1c30432dd17b21e1447d5f3f20/immunogenViewer.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /tmp/RtmpEyKP7F/file27d88149b509f3/immunogenViewer
installDir: /tmp/RtmpEyKP7F/file27d881513d7b05
isTarBall: TRUE
platform: unix
* 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 4.0 to 4.4.0.
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of immunogenViewer...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 94 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 292 lines
(28%) 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 is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 1 WARNINGS | 8 NOTES
See the immunogenViewer.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]