This page was generated on 2023-01-02 09:00:42 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
| 4165 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
CHECK results for oppti on palomino5
To the developers/maintainers of the oppti package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.
|
raw results
| oppti 1.13.0 (landing page) Abdulkadir Elmas
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022) |
git_url: https://git.bioconductor.org/packages/oppti |
git_branch: master |
git_last_commit: 357c91f |
git_last_commit_date: 2022-11-01 11:20:53 -0500 (Tue, 01 Nov 2022) |
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | |
Summary
Command output
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oppti.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings oppti_1.13.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/oppti.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oppti/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oppti' version '1.13.0'
* 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 whether package 'oppti' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* 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 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 ... NOTE
gqplot: no visible binding for global variable 'variable2'
gqplot: no visible binding for global variable 'variable1'
gqplot: no visible binding for global variable 'cupper'
gqplot: no visible binding for global variable 'clower'
markOut: no visible binding for global variable 'data'
per.test: no visible binding for global variable 'oppti.result'
per.test: no visible binding for global variable 'weight'
per.test: no visible binding for global variable '..density..'
Undefined global functions or variables:
..density.. clower cupper data oppti.result variable1 variable2
weight
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'markOut':
markOut
Code: function(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
marker.proc.list = NULL, dataset = "", num.omit.fit =
NULL, draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
ylab = "Observed", xlab = "Inferred", cohort.name =
NULL)
Docs: function(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
marker.proc.list = NULL, dataset = "", num.omit.fit =
NULL, draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
ylab = "Observed", xlab = "Inferred")
Argument names in code not in docs:
cohort.name
Codoc mismatches from documentation object 'oppti':
oppti
Code: function(data, mad.norm = FALSE, cohort.names = NULL, panel =
"global", panel.markers = NULL, tol.nas = 20, ku = 6,
miss.pstat = 0.4, demo.panels = FALSE, save.data =
FALSE, draw.sc.plots = FALSE, draw.vi.plots = FALSE,
draw.sc.markers = NULL, draw.ou.plots = FALSE,
draw.ou.markers = NULL, permutation.tests = TRUE,
n.per.test = 10, draw.per.test = FALSE,
plot.set.per.test = list(BRCA = c("ERBB2"), CCRCC =
c("ERBB2", "TP53")), verbose = FALSE)
Docs: function(data, mad.norm = FALSE, cohort.names = NULL, panel =
"global", panel.markers = NULL, tol.nas = 20, ku = 6,
miss.pstat = 0.4, demo.panels = FALSE, save.data =
FALSE, draw.sc.plots = FALSE, draw.vi.plots = FALSE,
draw.sc.markers = NULL, draw.ou.plots = FALSE,
draw.ou.markers = NULL, verbose = FALSE)
Argument names in code not in docs:
permutation.tests n.per.test draw.per.test plot.set.per.test
Mismatches in argument names:
Position: 16 Code: permutation.tests Docs: verbose
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test.R'
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 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/oppti.Rcheck/00check.log'
for details.
Installation output
oppti.Rcheck/00install.out
Tests output
oppti.Rcheck/tests/test.Rout
Example timings
oppti.Rcheck/oppti-Ex.timings