nebbiolo1 Summary
[top]
| Package: SpatialOmicsOverlay |
| Version: 0.99.4 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialOmicsOverlay |
| BuildTime: 3 minutes 19.41 seconds |
| CheckCommand: BiocCheckGitClone('SpatialOmicsOverlay') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings SpatialOmicsOverlay_0.99.4.tar.gz && BiocCheck('SpatialOmicsOverlay_0.99.4.tar.gz', `new-package`=TRUE) |
| CheckTime: 12 minutes 33.65 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2729.37 KiB |
| BuildID:: SpatialOmicsOverlay_20220422221224 |
| 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
[top]
===============================
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_0.99.4.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('SpatialOmicsOverlay')
===============================
─ BiocCheckVersion: 1.31.38
─ BiocVersion: 3.15
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘0.99.4’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialOmicsOverlay’ can be installed ... [20s/20s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [19s/19s] 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] NOTE
prepare_Rd: xmlExtraction.Rd:23-25: Dropping empty section \examples
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [479s/298s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readSpatialOverlay 92.050 3.316 83.572
changeImageColoring 29.791 1.447 13.675
plotSpatialOverlay 29.062 1.649 16.493
fluorLegend 28.644 1.561 15.968
recolor 27.858 1.623 15.876
cropTissue 27.750 1.579 14.928
addImageOmeTiff 27.236 1.530 13.653
changeColoringIntensity 27.125 1.322 13.959
flipX 25.707 1.970 17.638
add4ChannelImage 25.703 1.765 15.396
flipY 23.857 1.735 16.232
cropSamples 23.909 1.286 13.842
createMask 10.268 0.335 10.594
parseScanMetadata 8.103 0.360 3.382
fluorData 7.807 0.587 3.769
parseOverlayAttrs 7.449 0.578 3.500
physicalSizes 7.451 0.397 3.393
checkValidRes 5.879 0.365 2.388
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [369s/316s]
[369s/316s] 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 ... OK
* DONE
Status: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2604/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('SpatialOmicsOverlay_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.31.38
─ BiocVersion: 3.15
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/Rtmpf2boZM/file2a500c3da80fc6/SpatialOmicsOverlay
─ installDir: /tmp/Rtmpf2boZM/file2a500c59b478d2
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 6 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
* 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 4.2.0.
* 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...
* 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 sapply(); use vapply()
* 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
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 16
functions > 50 lines.
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
addImageFile.Rd, imageExtraction.Rd, moveCoords.Rd,
SpatialOverlay-class.Rd, SpatialPosition-class.Rd,
themeTransparent.Rd, xmlExtraction.Rd
* 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; 273 lines (4%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 800 lines
(12%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 11 NOTES
See the SpatialOmicsOverlay.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: SpatialOmicsOverlay |
| Version: 0.99.4 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialOmicsOverlay |
| BuildTime: 9 minutes 17.93 seconds |
| CheckCommand: BiocCheckGitClone('SpatialOmicsOverlay') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SpatialOmicsOverlay_0.99.4.tar.gz && BiocCheck('SpatialOmicsOverlay_0.99.4.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.96 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh SpatialOmicsOverlay_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 9.80 seconds |
| PackageFileSize: 2721.88 KiB |
| BuildID:: SpatialOmicsOverlay_20220422221224 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SpatialOmicsOverlay. 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. Checking Package status: -9. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
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_0.99.4.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('SpatialOmicsOverlay')
===============================
─ BiocCheckVersion: 1.31.38
─ BiocVersion: 3.15
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2604/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2604/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘0.99.4’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialOmicsOverlay’ can be installed ... [50s/50s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [52s/53s] 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 ... [1s/1s] NOTE
prepare_Rd: xmlExtraction.Rd:23-25: Dropping empty section \examples
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('SpatialOmicsOverlay_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.31.38
─ BiocVersion: 3.15
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpZOfge8/file11ca17929ff5c/SpatialOmicsOverlay
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpZOfge8/file11ca15b3c4789
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2604/d22002574c2fa3a41fbc4bd95073c416d6395f4b/SpatialOmicsOverlay.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
[12m/10m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readSpatialOverlay 207.517 4.763 207.184
add4ChannelImage 42.317 2.508 31.624
changeColoringIntensity 35.540 2.334 28.592
cropSamples 34.282 2.332 28.793
addImageOmeTiff 33.590 2.607 28.059
changeImageColoring 33.768 2.333 28.902
recolor 33.204 2.445 28.754
fluorLegend 32.874 2.135 27.409
flipY 32.390 2.229 26.957
cropTissue 31.880 2.454 26.689
flipX 31.744 2.500 26.544
plotSpatialOverlay 31.400 2.374 26.490
createMask 25.086 0.874 26.055
parseScanMetadata 7.203 0.684 5.724
fluorData 6.861 0.760 5.867
parseOverlayAttrs 6.821 0.760 5.941
physicalSizes 6.852 0.700 5.594
createCoordFile 7.376 0.036 7.469
checkValidRes 6.019 0.503 4.964
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 6 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
* 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 4.2.0.
* 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...
* 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 sapply(); use vapply()
* 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
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 16
functions > 50 lines.
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
addImageFile.Rd, imageExtraction.Rd, moveCoords.Rd,
SpatialOverlay-class.Rd, SpatialPosition-class.Rd,
themeTransparent.Rd, xmlExtraction.Rd
* 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; 273 lines (4%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 800 lines
(12%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 11 NOTES
See the SpatialOmicsOverlay.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SpatialOmicsOverlay_0.99.4.tar.gz'
>>>>>>>
* installing *source* package ‘SpatialOmicsOverlay’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘metadata<-’ in package ‘SpatialOmicsOverlay’
** 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 (SpatialOmicsOverlay)