===============================
R CMD BUILD
===============================
* checking for file ‘TOP/DESCRIPTION’ ... OK
* preparing ‘TOP’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘TOP/data/TOP_data_binary.Rda’
* building ‘TOP_0.99.2.tar.gz’
===============================
BiocCheckGitClone('TOP')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: TOP
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2971/7e7b4014478b9e7c89903a5204d6158d0f788424/TOP
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
R/.DS_Store
TOP.Rproj
* 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...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2971/7e7b4014478b9e7c89903a5204d6158d0f788424/TOP.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TOP/DESCRIPTION’ ... OK
* this is package ‘TOP’ version ‘0.99.2’
* 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 ‘TOP’ 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 ... WARNING
Subdirectory ‘data’ contains no data sets.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘assertthat’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [34s/34s] NOTE
Surv_TOP_CI: no visible binding for global variable ‘offset’
TOP_coefPlot: no visible binding for global variable ‘lambda.min’
TOP_coefPlot: no visible binding for global variable ‘Features’
TOP_lambdaPlot: no visible binding for global variable ‘variable’
TOP_lambdaPlot: no visible binding for global variable ‘value’
TOP_lambdaPlot: no visible binding for global variable ‘Feature’
TOP_model: no visible binding for global variable ‘value’
TOP_model: no visible binding for global variable ‘Organ’
TOP_model: no visible binding for global variable ‘n’
TOP_model: no visible binding for global variable ‘freq’
TOP_model: no visible binding for global variable ‘sd’
TOP_survival: no visible binding for global variable ‘coef’
TOP_survival: no visible binding for global variable ‘value’
TOP_survival: no visible binding for global variable ‘freq’
TOP_survival: no visible binding for global variable ‘sd’
TOP_survival: no visible binding for global variable ‘.’
TOP_survival: no visible binding for global variable ‘Organ’
TOP_survival: no visible binding for global variable ‘n’
TOP_survivalPrediction: no visible binding for global variable ‘offset’
coefNetworkPlot: no visible binding for global variable ‘Features’
coefNetworkPlot: no visible binding for global variable ‘lambda.min’
coefNetworkPlot: no visible binding for global variable ‘score’
colCoxTests_combine: no visible binding for global variable ‘coef’
colCoxTests_combine: no visible binding for global variable ‘Pathways’
extractAUC: no visible binding for global variable ‘variable’
extractAUC: no visible binding for global variable ‘value’
filterFeatures: no visible binding for global variable ‘Pathways’
simplenetworkPlot: no visible binding for global variable ‘Features’
simplenetworkPlot: no visible binding for global variable ‘lambda.min’
simplenetworkPlot: no visible binding for global variable ‘coef_abs’
simplenetworkPlot: no visible binding for global variable ‘from’
simplenetworkPlot: no visible binding for global variable ‘to’
simplenetworkPlot: no visible binding for global variable ‘name’
Undefined global functions or variables:
. Feature Features Organ Pathways coef coef_abs freq from lambda.min
n name offset score sd to value variable
Consider adding
importFrom("stats", "coef", "offset", "sd")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'filterFeatures.Rd':
\examples lines wider than 100 characters:
y_list <- y_list <- lapply(y_list, function(x){x <- factor(x, levels = c("1", "0"), labels = c("Yes", "No"))})
These lines will be truncated in the PDF manual.
* 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 ... WARNING
'data(package=)' call not declared from: ‘CPOP’
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘TOP_data_binary.Rda’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] ERROR
Running examples in ‘TOP-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ROC_Plot
> ### Title: ROC_Plot
> ### Aliases: ROC_Plot
>
> ### ** Examples
>
> data(cpop_data_binary, package = "CPOP")
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘CPOP’
Calls: data -> find.package
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2971/7e7b4014478b9e7c89903a5204d6158d0f788424/TOP.Rcheck/00check.log’
for details.
===============================
BiocCheck('TOP_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: TOP
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/Rtmpo1SGSw/file32978310386a17/TOP
─ installDir: /tmp/Rtmpo1SGSw/file32978376fa6e8d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2971/7e7b4014478b9e7c89903a5204d6158d0f788424/TOP.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.3.0.
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TOP...
* 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
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 7% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 109 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 119 lines
(6%) 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...
* 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 18 NOTES
See the TOP.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.