===============================
BiocCheckGitClone('poem')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/6724bd056d098cd1ee85f397c25895ff2005f786/poem
→ BiocVersion: 3.21
→ Package: poem
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/6724bd056d098cd1ee85f397c25895ff2005f786/poem.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/6724bd056d098cd1ee85f397c25895ff2005f786/poem
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3618/6724bd056d098cd1ee85f397c25895ff2005f786/poem.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘poem/DESCRIPTION’ ... OK
* this is package ‘poem’ version ‘0.99.6’
* 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 ‘poem’ 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
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘SpatialExperiment’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [42s/42s] NOTE
getSpatialExternalMetrics,SpatialExperiment: no visible global function
definition for ‘colData’
getSpatialInternalMetrics,SpatialExperiment: no visible global function
definition for ‘colData’
Undefined global functions or variables:
colData
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown packages ‘FuzzyPartitionMetrics()’, ‘fuzzyHardMetrics()’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'getSpatialInternalMetrics.Rd'
‘alpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] INFO
Note: found 2 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] ERROR
Running examples in ‘poem-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getSpatialExternalMetrics
> ### Title: Calculate Spatial External Metrics
> ### Aliases: getSpatialExternalMetrics
> ### getSpatialExternalMetrics,missing-method
> ### getSpatialExternalMetrics,SpatialExperiment-method
>
> ### ** Examples
>
> # Example with individual components
> data(sp_toys)
> data <- sp_toys
> getSpatialExternalMetrics(true=data$label, pred=data$p1,
+ location=data[,c("x", "y")], k=6, level="class")
Comparing between a fuzzy truth and a hard prediction...
Standard error of the mean NDC across permutations:0.000313
SpatialWH SpatialAWH SpatialWC SpatialAWC class cluster
1 NA NA 0.8078698 0.5941529 1 NA
2 NA NA 1.0000000 1.0000000 2 NA
3 1.0000000 1.0000000 NA NA NA 1
4 0.8323893 0.6495502 NA NA NA 2
>
> # Example with SpatialExperiment object
> se_object <- SpatialExperiment::SpatialExperiment(assays=matrix(NA,
+ ncol = nrow(data[,c("x", "y")]),
+ nrow = ncol(data[,c("x", "y")])),
+ spatialCoords=as.matrix(data[,c("x", "y")]))
> colData(se_object) <- cbind(colData(se_object), data.frame(true=data$label,
+ pred=data$p1))
Error in colData(se_object) : could not find function "colData"
Calls: cbind
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[15s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3618/6724bd056d098cd1ee85f397c25895ff2005f786/poem.Rcheck/00check.log’
for details.
===============================
BiocCheck('poem_0.99.6.tar.gz')
===============================
── Installing poem ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── poem session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp46DVQQ/file1b3956c995c0a/poem
→ BiocVersion: 3.21
→ Package: poem
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/6724bd056d098cd1ee85f397c25895ff2005f786/poem.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmp46DVQQ/file1b3956c995c0a/poem
→ installDir: /tmp/Rtmp46DVQQ/file1b3956495a23e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on poem ───────────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.0 to 4.5.0.
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (22%).
* Checking for pinned package versions in DESCRIPTION...
* 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 poem...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/CDbw.R (line 57, column 5)
• ...
• print() in R/CDbw.R (line 134, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/fuzzyPartitionMetrics.R (line 747, column 15)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/getSpatialExternalMetrics.R (line 94, column 20)
• R/getSpatialExternalMetrics.R (line 97, column 20)
• R/getSpatialInternalMetrics.R (line 81, column 20)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/fuzzyPartitionMetrics.R (line 181, column 13)
• R/fuzzyPartitionMetrics.R (line 411, column 13)
• R/fuzzyPartitionMetrics.R (line 607, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/simulation.R (line 51, column 14)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• CDbw() (R/CDbw.R): 146 lines
• ...
• getPartitionClassMetrics() (R/getPartitionClassMetrics.R): 113 lines
* Checking man page documentation...
Registered S3 method overwritten by 'e1071':
method from
print.fclust fclust
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• fuzzyPartitionMetrics.Rd
• matchSets.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 101 lines (2%) are > 80 characters long.
First few lines:
• R/getFuzzyPartitionMetrics.R#L147 returnE ...
• ...
• vignettes/PoemOnSpatialExperiment.Rmd#L459 The internal metrics can also be
calcula ...
i NOTE: Consider multiples of 4 spaces for line indents; 1909 lines (38%) are
not.
First few lines:
• R/CDbw.R#L42 clusterstdev=TRUE, trac ...
• ...
• vignettes/PoemOnSpatialExperiment.Rmd#L477 theme_bw() + labs(x="", y="",
color="E ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the poem.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.