merida1 Summary
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| Package: SpatialOmicsOverlay |
| Version: 0.99.15 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialOmicsOverlay |
| BuildTime: 0 minutes 20.92 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: SpatialOmicsOverlay_20230213205358 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SpatialOmicsOverlay. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 1. Build Package status: 1. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* preparing ‘SpatialOmicsOverlay’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘SpatialOmicsOverlay’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in fun(libname, pkgname) :
JAVA_HOME is set incorrectly! Ingoring.
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Warning in system("/usr/libexec/java_home", intern = TRUE) :
running command '/usr/libexec/java_home' had status 1
Warning in fun(libname, pkgname) :
Cannot find JVM library 'NA/lib/server/libjvm.dylib'
Install Java and/or check JAVA_HOME (if in doubt, do NOT set it, it will be detected)
Error: .onLoad failed in loadNamespace() for 'rJava', details:
call: fun(libname, pkgname)
error: JVM could not be found
Execution halted
ERROR: lazy loading failed for package ‘SpatialOmicsOverlay’
* removing ‘/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpA3ZNrx/Rinstf4825fe1f10d/SpatialOmicsOverlay’
-----------------------------------
ERROR: package installation failed
merida1 CHECK output
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merida1 BUILD BIN output
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nebbiolo1 Summary
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| Package: SpatialOmicsOverlay |
| Version: 0.99.15 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialOmicsOverlay |
| BuildTime: 7 minutes 58.20 seconds |
| CheckCommand: BiocCheckGitClone('SpatialOmicsOverlay') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2604/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2604/a17859dfa822444211af943e6e1f63702662311f/SpatialOmicsOverlay.install-out.txt SpatialOmicsOverlay_0.99.15.tar.gz && BiocCheck('SpatialOmicsOverlay_0.99.15.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 41.77 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2860.59 KiB |
| BuildID:: SpatialOmicsOverlay_20230213205358 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SpatialOmicsOverlay. 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. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* preparing ‘SpatialOmicsOverlay’:
* 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 ‘SpatialOmicsOverlay_0.99.15.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('SpatialOmicsOverlay')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.15
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/a17859dfa822444211af943e6e1f63702662311f/SpatialOmicsOverlay
─ 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/2604/a17859dfa822444211af943e6e1f63702662311f/SpatialOmicsOverlay.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 ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘0.99.15’
* 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 ‘SpatialOmicsOverlay’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/10s] 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 ... [38s/37s] NOTE
plotSpatialOverlay: no visible binding for global variable ‘xcoor’
plotSpatialOverlay: no visible binding for global variable ‘ycoor’
plotSpatialOverlay: no visible binding for global variable ‘sampleID’
plotSpatialOverlay: no visible binding for global variable ‘Target’
scaleBarPrinting: no visible binding for global variable ‘X’
scaleBarPrinting: no visible binding for global variable ‘Y’
Undefined global functions or variables:
Target X Y sampleID xcoor ycoor
* checking Rd files ... [0s/0s] WARNING
checkRd: (5) SpatialOverlay-class.Rd:91-93: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:94-96: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:97-99: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:100-102: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:103-105: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:106-108: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:109-111: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:112-115: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:116-118: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:119-122: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:123-125: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:126-128: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:129-131: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:132-134: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:135-137: \item in \describe must have non-empty label
checkRd: (5) SpatialOverlay-class.Rd:138-140: \item in \describe must have non-empty label
checkRd: (5) SpatialPosition-class.Rd:59-61: \item in \describe must have non-empty label
checkRd: (5) SpatialPosition-class.Rd:62-64: \item in \describe must have non-empty label
checkRd: (5) SpatialPosition-class.Rd:65-67: \item in \describe must have non-empty label
* 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 ... [33s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [396s/337s]
[396s/337s] 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 ... [3s/3s] OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2604/a17859dfa822444211af943e6e1f63702662311f/SpatialOmicsOverlay.Rcheck/00check.log’
for details.
===============================
BiocCheck('SpatialOmicsOverlay_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.15
─ sourceDir: /tmp/RtmpDd023i/file1ccdabf7d55/SpatialOmicsOverlay
─ installDir: /tmp/RtmpDd023i/file1ccda536816aa
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/a17859dfa822444211af943e6e1f63702662311f/SpatialOmicsOverlay.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 4.1.0 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...
* 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...
* 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 SpatialOmicsOverlay...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 99 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 89% 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; 235 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 545 lines
(12%) 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 ──
1 ERRORS | 0 WARNINGS | 10 NOTES
See the SpatialOmicsOverlay.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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