merida1 Summary
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Package: SPOTlight |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SPOTlight |
BuildTime: 2 minutes 26.94 seconds |
CheckCommand: BiocCheckGitClone('SPOTlight') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SPOTlight_0.99.0.tar.gz && BiocCheck('SPOTlight_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 10.19 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh SPOTlight_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 23.55 seconds |
PackageFileSize: 3154.48 KiB |
BuildID:: SPOTlight_20220120163316 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SPOTlight. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 0. 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 ‘SPOTlight/DESCRIPTION’ ... OK
* preparing ‘SPOTlight’:
* 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 ‘SPOTlight_0.99.0.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('SPOTlight')
===============================
This is BiocCheckGitClone version 1.31.28. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2488/SPOTlight_20220120163316/SPOTlight.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘SeuratData’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2488/SPOTlight_20220120163316/SPOTlight.Rcheck/00check.log’
for details.
===============================
BiocCheck('SPOTlight_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.28. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2488/SPOTlight_20220120163316/SPOTlight_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpN7iRg3/file1369d1aba3c23/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 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...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Sequencing, Transcriptomics, Regression
See http://bioconductor.org/developers/how-to/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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SPOTlight...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 3 functions > 50 lines.
The longest 5 functions are:
_anonymous_.59() (R/plotTopicProfiles.R, line 59): 68 lines
.train_nmf() (R/utils.R, line 92): 65 lines
.init_nmf() (R/utils.R, line 7): 60 lines
_anonymous_.59() (R/plotCorrelationMatrix.R, line 59): 47 lines
_anonymous_.54() (R/plotSpatialScatterpie.R, line 54): 47 lines
* Checking man page documentation...
* 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; 18 lines (1%) are > 80 characters
long.
First 6 lines:
man/plotSpatialScatterpie.Rd:23 \S4method{plotSpatialScatterpie}{Seurat...
man/plotTopicProfiles.Rd:11 \S4method{plotTopicProfiles}{NMF,character}...
man/SPOTlight.Rd:27 \S4method{SPOTlight}{Seurat,ANY}(x, y, ..., slot = ...
man/SPOTlight.Rd:35 \S4method{SPOTlight}{ANY,DelayedMatrix}(x, y, ..., ...
man/SPOTlight.Rd:37 \S4method{SPOTlight}{DelayedMatrix,ANY}(x, y, ..., ...
vignettes/SPOTlight_kidney.Rmd:7 - &CNAG-CRG National Center for Geno...
* NOTE: Consider multiples of 4 spaces for line indents, 96
lines(4%) are not.
First 6 lines:
man/data.Rd:28 with rows = genes, columns = single cells, and cell me...
man/data.Rd:29 (\code{colData}) column \code{type} containing group i...
man/data.Rd:31 with rows = genes, columns = single cells, and cell me...
man/data.Rd:32 (\code{colData}) column \code{type} containing group i...
man/data.Rd:34 rows and 3 columns: gene and type (group) identifier, ...
man/data.Rd:35 gene's weight = the proportion of counts accounted for...
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...
* 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...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 5
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SPOTlight_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘SPOTlight’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘plotImage’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotSpatialScatterpie’ with signature ‘"SpatialExperiment","ANY"’: no definition for class “SpatialExperiment”
** 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 (SPOTlight)
nebbiolo1 Summary
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Package: SPOTlight |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SPOTlight |
BuildTime: 1 minutes 46.93 seconds |
CheckCommand: BiocCheckGitClone('SPOTlight') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings SPOTlight_0.99.0.tar.gz && BiocCheck('SPOTlight_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 4.29 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3169.28 KiB |
BuildID:: SPOTlight_20220120163316 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SPOTlight. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. 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 ‘SPOTlight/DESCRIPTION’ ... OK
* preparing ‘SPOTlight’:
* 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 ‘SPOTlight_0.99.0.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('SPOTlight')
===============================
This is BiocCheckGitClone version 1.31.28. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2488/SPOTlight_20220120163316/SPOTlight.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘SeuratData’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2488/SPOTlight_20220120163316/SPOTlight.Rcheck/00check.log’
for details.
===============================
BiocCheck('SPOTlight_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.28. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2488/SPOTlight_20220120163316/SPOTlight_0.99.0.tar.gz" "/tmp/RtmpzEFof5/file2986062944d27f/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 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...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Sequencing, Transcriptomics, Regression
See http://bioconductor.org/developers/how-to/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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SPOTlight...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 3 functions > 50 lines.
The longest 5 functions are:
_anonymous_.59() (R/plotTopicProfiles.R, line 59): 68 lines
.train_nmf() (R/utils.R, line 92): 65 lines
.init_nmf() (R/utils.R, line 7): 60 lines
_anonymous_.59() (R/plotCorrelationMatrix.R, line 59): 47 lines
_anonymous_.54() (R/plotSpatialScatterpie.R, line 54): 47 lines
* Checking man page documentation...
* 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; 18 lines (1%) are > 80 characters
long.
First 6 lines:
man/plotSpatialScatterpie.Rd:23 \S4method{plotSpatialScatterpie}{Seurat...
man/plotTopicProfiles.Rd:11 \S4method{plotTopicProfiles}{NMF,character}...
man/SPOTlight.Rd:27 \S4method{SPOTlight}{Seurat,ANY}(x, y, ..., slot = ...
man/SPOTlight.Rd:35 \S4method{SPOTlight}{ANY,DelayedMatrix}(x, y, ..., ...
man/SPOTlight.Rd:37 \S4method{SPOTlight}{DelayedMatrix,ANY}(x, y, ..., ...
vignettes/SPOTlight_kidney.Rmd:7 - &CNAG-CRG National Center for Geno...
* NOTE: Consider multiples of 4 spaces for line indents, 96
lines(4%) are not.
First 6 lines:
man/data.Rd:28 with rows = genes, columns = single cells, and cell me...
man/data.Rd:29 (\code{colData}) column \code{type} containing group i...
man/data.Rd:31 with rows = genes, columns = single cells, and cell me...
man/data.Rd:32 (\code{colData}) column \code{type} containing group i...
man/data.Rd:34 rows and 3 columns: gene and type (group) identifier, ...
man/data.Rd:35 gene's weight = the proportion of counts accounted for...
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...
* 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...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 5
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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