===============================
BiocCheckGitClone('CytoMethIC')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: CytoMethIC
─ PackageVersion: 0.99.12
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3097/58e665ba6a17c652c6404b728bc234194c3fe2a9/CytoMethIC
─ 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...
* 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 results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3097/58e665ba6a17c652c6404b728bc234194c3fe2a9/CytoMethIC.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoMethIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoMethIC’ version ‘0.99.12’
* 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 ‘CytoMethIC’ 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 ... 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking whether startup messages can be suppressed ... [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 ... [27s/27s] OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] ERROR
Running examples in ‘CytoMethIC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmi_classify
> ### Title: The cmi_classify function takes in a model and a sample, and
> ### uses the model to classify it. This function supports randomForest,
> ### e1071::svm, xgboost, and keras/tensorflow models. For xgboost and
> ### keras models, the features used in classification as well as a label
> ### mapping must be provided for output.
> ### Aliases: cmi_classify
>
> ### ** Examples
>
>
> library(sesameData)
Loading sesameData.
> library(ExperimentHub)
> basedir = "https://github.com/zhou-lab/CytoMethIC_models/raw/main/models/"
>
> ## Cancer Type
> model = ExperimentHub()[["EH8395"]]
see ?CytoMethIC and browseVignettes('CytoMethIC') for documentation
loading from cache
> cmi_classify(openSesame(sesameDataGet("EPICv2.8.SigDF")[[1]]), model)
Error in openSesame(sesameDataGet("EPICv2.8.SigDF")[[1]]) :
could not find function "openSesame"
Calls: cmi_classify
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [46s/48s]
[46s/48s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading CytoMethIC.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_data.R:40:3'): infer_sex returns string ────────────────────────
Error: 'inferSex' is not an exported object from 'namespace:CytoMethIC'
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted
* 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 ... [2s/2s] OK
* DONE
Status: 2 ERRORs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3097/58e665ba6a17c652c6404b728bc234194c3fe2a9/CytoMethIC.Rcheck/00check.log’
for details.
===============================
BiocCheck('CytoMethIC_0.99.12.tar.gz')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: CytoMethIC
─ PackageVersion: 0.99.12
─ sourceDir: /tmp/RtmpOZ8pi0/file25f5bd726de50e/CytoMethIC
─ installDir: /tmp/RtmpOZ8pi0/file25f5bd10fd3fd0
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3097/58e665ba6a17c652c6404b728bc234194c3fe2a9/CytoMethIC.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 4.3.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* WARNING: Package files exceed the 5MB size limit.
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* 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 CytoMethIC...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 20% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* 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; 25 lines (8%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 11 lines
(4%) 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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 6 NOTES
See the CytoMethIC.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.