nebbiolo1 Summary
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| Package: SpatialOmicsOverlay |
| Version: 0.99.16 |
| 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 48.43 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/2604/340975f3de5bbc5a0115eb86c0be545649c7d646/SpatialOmicsOverlay.install-out.txt SpatialOmicsOverlay_0.99.16.tar.gz && BiocCheck('SpatialOmicsOverlay_0.99.16.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 31.68 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2860.62 KiB |
| BuildID:: SpatialOmicsOverlay_20230220202819 |
| 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_0.99.16.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('SpatialOmicsOverlay')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.16
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/340975f3de5bbc5a0115eb86c0be545649c7d646/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/2604/340975f3de5bbc5a0115eb86c0be545649c7d646/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 ‘0.99.16’
* 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 ... OK
* 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 ... [10s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/8s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [32s/32s] 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 ... [204s/137s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cropTissue 28.011 1.672 16.306
add4ChannelImage 25.252 1.693 17.479
addImageOmeTiff 23.690 1.391 14.914
readSpatialOverlay 21.955 1.226 17.173
recolor 19.575 1.158 14.617
parseOverlayAttrs 10.561 0.941 4.726
xmlExtraction 9.279 0.487 4.451
checkValidRes 9.151 0.571 3.927
parseScanMetadata 7.957 0.312 4.369
createMask 7.524 0.508 8.025
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [365s/318s]
[365s/319s] 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, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2604/340975f3de5bbc5a0115eb86c0be545649c7d646/SpatialOmicsOverlay.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('SpatialOmicsOverlay_0.99.16.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.16
─ sourceDir: /tmp/RtmpqdV86T/file1d65f63c9e98eb/SpatialOmicsOverlay
─ installDir: /tmp/RtmpqdV86T/file1d65f675683271
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/340975f3de5bbc5a0115eb86c0be545649c7d646/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. 19% of man pages use at least one of these tags.
* 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 | 9 NOTES
See the SpatialOmicsOverlay.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: SpatialOmicsOverlay |
| Version: 0.99.16 |
| 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 20.49 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: SpatialOmicsOverlay_20230220202819 |
| 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: 1. 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/RtmpqTLEut/Rinst169b55af3522f/SpatialOmicsOverlay’
-----------------------------------
ERROR: package installation failed
merida1 CHECK output
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merida1 BUILD BIN output
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