nebbiolo1 Summary
[top]
| Package: SPOTlight |
| Version: 0.99.8 |
| 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: 2 minutes 31.64 seconds |
| CheckCommand: BiocCheckGitClone('SPOTlight') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings SPOTlight_0.99.8.tar.gz && BiocCheck('SPOTlight_0.99.8.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 25.85 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2721.58 KiB |
| BuildID:: SPOTlight_20220315201042 |
| 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: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
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_0.99.8.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('SPOTlight')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2488/012b92feb081dd453fb3c6fc74d72960f79a6b2a/SPOTlight.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* 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 ‘0.99.8’
* 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 ‘SPOTlight’ can be installed ... [26s/26s] 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 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 ... [26s/26s] NOTE
plotImage,SpatialExperiment: no visible global function definition for
‘imgData’
plotSpatialScatterpie,SpatialExperiment-ANY: no visible global function
definition for ‘imgData’
plotSpatialScatterpie,SpatialExperiment-ANY: no visible binding for
global variable ‘spe’
plotSpatialScatterpie,matrix-matrix: no visible binding for global
variable ‘imagecol’
plotSpatialScatterpie,matrix-matrix: no visible binding for global
variable ‘imagerow’
runDeconvolution,Seurat: ... may be used in an incorrect context:
‘runDeconvolution(GetAssayData(x, slot, assay), ...)’
Undefined global functions or variables:
imagecol imagerow imgData spe
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [152s/153s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SPOTlight 92.627 8.719 102.668
plotTopicProfiles 6.862 0.271 7.134
runDeconvolution 5.742 0.173 5.915
trainNMF 5.337 0.048 5.386
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [83s/84s]
[83s/84s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2488/012b92feb081dd453fb3c6fc74d72960f79a6b2a/SPOTlight.Rcheck/00check.log’
for details.
===============================
BiocCheck('SPOTlight_0.99.8.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2488/012b92feb081dd453fb3c6fc74d72960f79a6b2a/SPOTlight_0.99.8.tar.gz" "/tmp/Rtmp33UjOQ/file16dde21d0cafd2/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_.164() (R/trainNMF.R, line 164): 69 lines
_anonymous_.57() (R/plotTopicProfiles.R, line 57): 58 lines
.init_nmf() (R/utils.R, line 6): 56 lines
plotCorrelationMatrix() (R/plotCorrelationMatrix.R, line 54):
44 lines
_anonymous_.53() (R/plotSpatialScatterpie.R, line 53): 43 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; 24 lines (1%) are > 80 characters
long.
First 6 lines:
R/plotTopicProfiles.R:68 setequal(colnames(basis(x)), paste...
R/SPOTlight.R:270 list("mat" = res[["mat"]], "res_ss" = res[["r...
man/plotSpatialScatterpie.Rd:23 \S4method{plotSpatialScatterpie}{Seurat...
man/plotTopicProfiles.Rd:11 \S4method{plotTopicProfiles}{NMFfit,charact...
man/SPOTlight.Rd:27 \S4method{SPOTlight}{Seurat,ANY}(x, y, ..., slot = ...
man/SPOTlight.Rd:35 \S4method{SPOTlight}{ANY,DelayedMatrix}(x, y, ..., ...
* NOTE: Consider multiples of 4 spaces for line indents, 136
lines(5%) 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...
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.
Summary:
ERROR count: 0
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
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
| Package: SPOTlight |
| Version: 0.99.8 |
| 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: 4 minutes 40.30 seconds |
| CheckCommand: BiocCheckGitClone('SPOTlight') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SPOTlight_0.99.8.tar.gz && BiocCheck('SPOTlight_0.99.8.tar.gz', `new-package`=TRUE) |
| CheckTime: 11 minutes 51.77 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh SPOTlight_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 44.98 seconds |
| PackageFileSize: 2690.54 KiB |
| BuildID:: SPOTlight_20220315201042 |
| 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: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 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_0.99.8.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('SPOTlight')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2488/012b92feb081dd453fb3c6fc74d72960f79a6b2a/SPOTlight.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* 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 ‘0.99.8’
* 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 ‘SPOTlight’ can be installed ... [44s/44s] 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 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 ... [46s/46s] NOTE
plotImage,SpatialExperiment: no visible global function definition for
‘imgData’
plotSpatialScatterpie,SpatialExperiment-ANY: no visible global function
definition for ‘imgData’
plotSpatialScatterpie,SpatialExperiment-ANY: no visible binding for
global variable ‘spe’
plotSpatialScatterpie,matrix-matrix: no visible binding for global
variable ‘imagecol’
plotSpatialScatterpie,matrix-matrix: no visible binding for global
variable ‘imagerow’
runDeconvolution,Seurat: ... may be used in an incorrect context:
‘runDeconvolution(GetAssayData(x, slot, assay), ...)’
Undefined global functions or variables:
imagecol imagerow imgData spe
* checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [225s/232s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SPOTlight 137.050 8.230 152.602
plotTopicProfiles 13.979 0.042 14.040
runDeconvolution 10.618 0.038 10.669
trainNMF 10.519 0.045 10.572
data 9.577 0.038 9.627
plotImage 6.158 0.711 6.998
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [141s/142s]
[141s/142s] 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: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2488/012b92feb081dd453fb3c6fc74d72960f79a6b2a/SPOTlight.Rcheck/00check.log’
for details.
===============================
BiocCheck('SPOTlight_0.99.8.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2488/012b92feb081dd453fb3c6fc74d72960f79a6b2a/SPOTlight_0.99.8.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmphOZ6ie/file10c4a7ff7a17f/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_.164() (R/trainNMF.R, line 164): 69 lines
_anonymous_.57() (R/plotTopicProfiles.R, line 57): 58 lines
.init_nmf() (R/utils.R, line 6): 56 lines
plotCorrelationMatrix() (R/plotCorrelationMatrix.R, line 54):
44 lines
_anonymous_.53() (R/plotSpatialScatterpie.R, line 53): 43 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; 24 lines (1%) are > 80 characters
long.
First 6 lines:
R/plotTopicProfiles.R:68 setequal(colnames(basis(x)), paste...
R/SPOTlight.R:270 list("mat" = res[["mat"]], "res_ss" = res[["r...
man/plotSpatialScatterpie.Rd:23 \S4method{plotSpatialScatterpie}{Seurat...
man/plotTopicProfiles.Rd:11 \S4method{plotTopicProfiles}{NMFfit,charact...
man/SPOTlight.Rd:27 \S4method{SPOTlight}{Seurat,ANY}(x, y, ..., slot = ...
man/SPOTlight.Rd:35 \S4method{SPOTlight}{ANY,DelayedMatrix}(x, y, ..., ...
* NOTE: Consider multiples of 4 spaces for line indents, 136
lines(5%) 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...
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.
Summary:
ERROR count: 0
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
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SPOTlight_0.99.8.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)