This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup"
| 4461 |
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 |
| cancerclass 1.48.0 (landing page) Daniel Kosztyla
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
git_url: https://git.bioconductor.org/packages/cancerclass |
git_branch: RELEASE_3_19 |
git_last_commit: 12491a7 |
git_last_commit_date: 2024-04-30 10:27:46 -0400 (Tue, 30 Apr 2024) |
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | |
CHECK results for cancerclass on kjohnson3
To the developers/maintainers of the cancerclass package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
|
raw results
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cancerclass.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cancerclass_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cancerclass.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cancerclass/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cancerclass’ version ‘1.48.0’
* 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 ‘cancerclass’ can be installed ... WARNING
Found the following significant warnings:
help.c:335:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cancerclass.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL 3
Standardizable: TRUE
Standardized license specification:
GPL-3
* 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 ... 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
‘binom’ ‘Biobase’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘cancerclass/R/cancerclass-internal.R’:
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
calc.auc: no visible global function definition for ‘integrate’
calc.auc : <anonymous>: no visible global function definition for
‘approx’
calc.roc: no visible global function definition for ‘binom.confint’
fit: no visible global function definition for ‘pData’
fit: no visible global function definition for ‘featureData’
fit: no visible global function definition for ‘exprs’
fit: no visible binding for global variable ‘methods’
get.prop: no visible global function definition for ‘binom.confint’
loo: no visible global function definition for ‘pData’
nvalidate: no visible global function definition for ‘pData’
nvalidate: no visible global function definition for ‘featureData’
nvalidate: no visible global function definition for ‘exprs’
nvalidate: no visible binding for global variable ‘methods’
prepare: no visible global function definition for ‘pData’
prepare: no visible global function definition for ‘exprs’
prepare: no visible global function definition for ‘exprs<-’
validate: no visible global function definition for ‘pData’
validate: no visible global function definition for ‘featureData’
validate: no visible global function definition for ‘exprs’
validate: no visible binding for global variable ‘methods’
plot,nvalidation: no visible global function definition for ‘grey’
plot,nvalidation: no visible global function definition for ‘par’
plot,nvalidation: no visible global function definition for ‘barplot’
plot,nvalidation: no visible global function definition for ‘legend’
plot,nvalidation : <anonymous>: no visible global function definition
for ‘quantile’
plot,nvalidation: no visible global function definition for ‘abline’
plot,nvalidation: no visible global function definition for ‘lines’
plot,prediction: no visible global function definition for ‘t.test’
plot,prediction: no visible global function definition for ‘par’
plot,prediction: no visible global function definition for ‘hist’
plot,prediction: no visible global function definition for ‘legend’
plot,prediction: no visible global function definition for ‘barplot’
plot,prediction: no visible global function definition for ‘lines’
plot,prediction: no visible global function definition for ‘abline’
plot,prediction: no visible global function definition for ‘glm’
plot,prediction: no visible binding for global variable ‘binomial’
plot,prediction: no visible global function definition for ‘pchisq’
plot,prediction: no visible global function definition for ‘qnorm’
plot,prediction: no visible global function definition for ‘points’
plot,predictor: no visible global function definition for ‘barplot’
plot,validation: no visible global function definition for ‘grey’
plot,validation: no visible global function definition for ‘par’
plot,validation: no visible global function definition for ‘barplot’
plot,validation: no visible global function definition for ‘legend’
plot,validation : <anonymous>: no visible global function definition
for ‘quantile’
plot,validation: no visible global function definition for ‘abline’
plot,validation: no visible global function definition for ‘lines’
plot3d,nvalidation: no visible global function definition for ‘persp’
plot3d,validation: no visible global function definition for ‘persp’
predict,predictor: no visible global function definition for ‘pData’
predict,predictor: no visible global function definition for ‘exprs’
summary,prediction: no visible global function definition for
‘fisher.test’
Undefined global functions or variables:
abline approx barplot binom.confint binomial exprs exprs<-
featureData fisher.test glm grey hist integrate legend lines methods
par pchisq pData persp points qnorm quantile t.test
Consider adding
importFrom("graphics", "abline", "barplot", "hist", "legend", "lines",
"par", "persp", "points")
importFrom("grDevices", "grey")
importFrom("stats", "approx", "binomial", "fisher.test", "glm",
"integrate", "pchisq", "qnorm", "quantile", "t.test")
importFrom("utils", "methods")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) predictor-class.Rd:25: Lost braces
25 | \code{plot}{A plot method is only avaiable for the score "zeta" that is a linear combination of features.}
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Objects in \usage without \alias in Rd file 'cancerclass-internal.Rd':
‘.onLoad’ ‘.initFoo’
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GOLUB 6.45 0.604 7.065
* 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 ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cancerclass.Rcheck/00check.log’
for details.
Installation output
cancerclass.Rcheck/00install.out
Tests output
Example timings
cancerclass.Rcheck/cancerclass-Ex.timings